Release Notes For GenBank Release 135
GBREL.TXT Genetic Sequence Data Bank
April 15 2003
NCBI-GenBank Flat File Release 135.0
Distribution Release Notes
24027936 loci, 31099264455 bases, from 24027936 reported sequences
This document describes the format and content of the flat files that
comprise releases of the GenBank database. If you have any questions or
comments about GenBank or this document, please contact NCBI via email
at [email protected] or:
GenBank
National Center for Biotechnology Information
National Library of Medicine, 38A, 8N805
8600 Rockville Pike
Bethesda, MD 20894
USA
Phone: (301) 496-2475
Fax: (301) 480-9241
==========================================================================
TABLE OF CONTENTS
==========================================================================
1. INTRODUCTION
1.1 Release 135.0
1.2 Cutoff Date
1.3 Important Changes in Release 135.0
1.4 Upcoming Changes
1.5 Request for Direct Submission of Sequence Data
1.6 Organization of This Document
2. ORGANIZATION OF DATA FILES
2.1 Overview
2.2 Files
2.2.1 File Descriptions
2.2.5 File Sizes
2.2.6 Per-Division Statistics
2.2.7 Selected Per-Organism Statistics
2.2.8 Growth of GenBank
3. FILE FORMATS
3.1 File Header Information
3.2 Directory Files
3.2.1 Short Directory File
3.3 Index Files
3.3.1 Accession Number Index File
3.3.2 Keyword Phrase Index File
3.3.3 Author Name Index File
3.3.4 Journal Citation Index File
3.3.5 Gene Name Index
3.4 Sequence Entry Files
3.4.1 File Organization
3.4.2 Entry Organization
3.4.3 Sample Sequence Data File
3.4.4 LOCUS Format
3.4.5 DEFINITION Format
3.4.5.1 DEFINITION Format for NLM Entries
3.4.6 ACCESSION Format
3.4.7 VERSION Format
3.4.8 KEYWORDS Format
3.4.9 SEGMENT Format
3.4.10 SOURCE Format
3.4.11 REFERENCE Format
3.4.12 FEATURES Format
3.4.12.1 Feature Key Names
3.4.12.2 Feature Location
3.4.12.3 Feature Qualifiers
3.4.12.4 Cross-Reference Information
3.4.12.5 Feature Table Examples
3.4.13 ORIGIN Format
3.4.14 SEQUENCE Format
4. ALTERNATE RELEASES
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
6. GENBANK ADMINISTRATION
6.1 Registered Trademark Notice
6.2 Citing GenBank
6.3 GenBank Distribution Formats and Media
6.4 Other Methods of Accessing GenBank Data
6.5 Request for Corrections and Comments
6.6 Credits and Acknowledgments
6.7 Disclaimer
==========================================================================
1. INTRODUCTION
1.1 Release 135.0
The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is responsible
for producing and distributing the GenBank Sequence Database. NCBI handles
all GenBank direct submissions and authors are advised to use the address
below. Submitters are encouraged to use the free Sequin software package
for sending sequence data, or the newly developed World Wide Web submission
form. See Section 1.5 below for details.
*****************************************************************************
The address for direct submissions to GenBank is:
GenBank Submissions
National Center for Biotechnology Information
Bldg 38A, Rm. 8N-803
8600 Rockville Pike
Bethesda, MD 20894
E-MAIL: [email protected]
Updates and changes to existing GenBank records:
E-MAIL: [email protected]
URL for the new GenBank submission tool - BankIt - on the World Wide Web:
http://www.ncbi.nlm.nih.gov/
(see Section 1.5 for additional details about submitting data to GenBank.)
*****************************************************************************
GenBank Release 135.0 is a release of sequence data by NCBI in the GenBank
flatfile format. GenBank is a component of a tri-partite, international
collaboration of sequence databases in the U.S., Europe, and Japan. The
collaborating databases in Europe are the European Molecular Biology Laboratory
(EMBL) at Hinxton Hall, UK, and the DNA Database of Japan (DDBJ) in Mishima,
Japan. Patent sequences are incorporated through arrangements with the
U.S. Patent and Trademark Office, and via the collaborating international
databases from other international patent offices. The database is converted
to various output formats, including the Flat File and Abstract Syntax Notation 1
(ASN.1) versions. The ASN.1 and Flat File forms of the data are available at
NCBI's anonymous FTP server: ftp.ncbi.nih.gov .
1.2 Cutoff Date
This full release, 135.0, incorporates data available to the collaborating
databases as of April 9, 2003. For more recent data, users are advised to:
o Download the GenBank Update files by anonymous FTP to 'ftp.ncbi.nih.gov':
ftp://ftp.ncbi.nih.gov/ncbi-asn1 (ASN.1 format)
ftp://ftp.ncbi.nih.gov/genbank (flatfile format)
Mirrors of the GenBank FTP site at the NCBI are available from the San Diego
Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
Some users who experience slow FTP transfers of large files (entire releases,
the GenBank Cumulative Update, etc) might realize an improvement in transfer
rates from these alternate sites when traffic at the NCBI is high.
o Use the interactive Network-Entrez or Web-Entrez applications to query
the 'Entrez: Nucleotides' database (see Section 6.4 of this document).
1.3 Important Changes in Release 135.0
1.3.1 Organizational changes
The total number of sequence data files increased by 17 with this release:
- the BCT division is now comprised of 7 files (+1)
- the EST division is now comprised of 244 files (+4)
- the GSS division is now comprised of 70 files (+4)
- the HTG division is now comprised of 62 files (+4)
- the INV division is now comprised of 6 files (+1)
- the PAT division is now comprised of 8 files (+1)
- the PRI division is now comprised of 25 files (+1)
- the ROD division is now comprised of 7 files (+1)
1.3.2 New /mol_type qualifier
As of the April 2003 GenBank Release (135.0), a new source feature
qualifier called /mol_type will begin to be used for source features.
This qualifier will be used to indicate the in-vivo biological state
of the sequence presented in a database record.
The preliminary definition for /segment is :
Qualifier /mol_type=
Definition in vivo molecule type
Value format "text"
Example /mol_type="genomic DNA",
Comment text limited to "genomic DNA", "genomic RNA", "mRNA" (incl EST),
"tRNA", "rRNA", "snoRNA", "snRNA", "scRNA", "pre-mRNA",
"other RNA" (incl. synthetic), "other DNA" (incl. synthetic),
"unassigned DNA" (incl. unknown),"unassigned RNA" (incl. unknown)
In-vivo molecule type information is already presented on the LOCUS
line of the GenBank flatfile format. However, introducing /mol_type
in the Feature Table will make the exchange of this information among
DDBJ, EMBL, and GenBank more complete and accurate.
NOTE: /mol_type will eventually be a mandatory qualifier for the source
feature, probably by June 2003.
1.3.3 New /segment qualifier
As of the April 2003 GenBank Release (135.0), a new source feature
qualifier called /segment will begin to be used for source features.
In the absence of a more suitable way to annotate viral segments, this
information had either not been included in database entries, or had been
annotated incorrectly (e.g. using /chromosome, /map etc). This new
qualifier addresses that lack.
The preliminary definition for /segment is :
Qualifier /segment=
Definition name of viral or phage segment sequenced
Value format "text"
Example /segment="6"
1.3.4 New /locus_tag qualifier
As of the April 2003 GenBank Release (135.0), a new source feature
qualifier called /locus_tag will begin to be used.
Many complete-genome sequencing projects use solely computational
methods to predict coding regions and genes. The /locus_tag qualifier
provides a method for identifying and tracking the results of such
computations, without utilizing existing qualifiers such as /gene .
These 'locus tags' are systematically assigned, and do not necessarily
reflect gene name/symbol conventions in experimental literature. Hence
the introduction of this new qualifier.
The preliminary definition for /locus_tag is :
Qualifier: /locus_tag
Definition: feature tag assigned for tracking purposes
Value Format: "text" (single token)
Example: /locus_tag="RSc0382"
/locus_tag="YPO0002"
Comment: /locus_tag can be used with any feature where /gene
is valid;
1.3.5 GSS File Header Problem
GSS sequences at GenBank are maintained in one of two different systems,
depending on their origin. One recent change to release processing involves
the parallelization of the dumps from those systems. Because the second dump
(for example) has no prior knowledge of exactly how many GSS files will be
dumped from the first, it doesn't know how to number it's own output files.
There is thus a discrepancy between the filenames and file headers of nine
GSS flatfiles in Release 135.0. Consider the gbgss60.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
April 15 2003
NCBI-GenBank Flat File Release 135.0
GSS Sequences (Part 1)
86691 loci, 65546719 bases, from 86691 reported sequences
Here, the filename and part number in the header is "1", though the file
has been renamed as "60" based on the files dumped from the other system.
We will work to resolve this discrepancy in future releases, but the
priority is certainly much lower than many other tasks.
1.4 Upcoming Changes
No changes to the format of GenBank releases are currently scheduled.
1.5 Request for Direct Submission of Sequence Data
A successful GenBank requires that sequence data enter the database as
soon as possible after publication, that the annotations be as complete as
possible, and that the sequence and annotation data be accurate. All
three of these requirements are best met if authors of sequence data
submit their data directly to GenBank in a usable form. It is especially
important that these submissions be in computer-readable form.
GenBank must rely on direct author submission of data to ensure that
it achieves its goals of completeness, accuracy, and timeliness. To
assist researchers in entering their own sequence data, GenBank
provides a WWW submission tool called BankIt, as well as a stand-alone
software package called Sequin. BankIt and Sequin are both easy-to-use
programs that enable authors to enter a sequence, annotate it, and
submit it to GenBank. Through the international collaboration of DNA
sequence databases, GenBank submissions are forwarded daily for inclusion
in the EMBL and DDBJ databases.
SEQUIN. Sequin is an interactive, graphically-oriented program based
on screen forms and controlled vocabularies that guides you through the
process of entering your sequence and providing biological and
bibliographic annotation. Sequin is designed to simplify the sequence submission
process, and to provide increased data handling capabilities to accomodate
very long sequences, complex annotations, and robust error checking. E-mail
the completed submission file to : [email protected]
Sequin is provided for Macintosh, PC/Windows, UNIX and VMS computers.
It is available by annonymous ftp from ftp.ncbi.nih.gov; login as
anonymous and use your e-mail address as the password. It is located in
the sequin directory. Or direct your web browser to this URL:
ftp://ftp.ncbi.nih.gov/sequin
BANKIT. BankIt provides a simple forms approach for submitting your
sequence and descriptive information to GenBank. Your submission will
be submitted directly to GenBank via the World Wide Web, and
immediately forwarded for inclusion in the EMBL and DDBJ databases.
BankIt may be used with Netscape, Internet Explorer, and other common
WWW clients. You can access BankIt from GenBank's home page:
http://www.ncbi.nlm.nih.gov/
AUTHORIN. Authorin sequence submissions are no longer accepted by
GenBank, and the Authorin application is no longer distributed by NCBI.
If you have questions about GenBank submissions or any of the data
submission tools, contact NCBI at: [email protected] or 301-496-2475.
1.6 Organization of This Document
The second section describes the contents of GenBank releases. The third
section illustrates the formats of the flat files. The fourth section
describes other versions of the data, the fifth section identifies known prob-
lems, and the sixth contains administrative details.
2. ORGANIZATION OF DATA FILES
2.1 Overview
GenBank releases consist of a set of ASCII text files, most of which
contain sequence data. A few supplemental "index" files are also supplied,
containing comprehensive lists of author names, journal citations,
gene names, and keywords, along with the accession numbers of the records
in which they can be found (see Section 3.3). The line-lengths of
these files is variable.
2.2 Files
This GenBank flat file release consists of 481 files. The lists
that follow describe each of the files included in the distribution.
Their sizes and base pair content are also summarized.
2.2.1 File Descriptions
1. gbrel.txt - Release notes (this document).
2. gbsdr.txt - Short directory of the data bank.
3. gbacc.idx - Index of the entries according to accession number.
4. gbkey.idx - Index of the entries according to keyword phrase.
5. gbaut1.idx - Index of the entries according to author, part 1.
6. gbaut2.idx - Index of the entries according to author, part 2.
7. gbaut3.idx - Index of the entries according to author, part 3.
8. gbaut4.idx - Index of the entries according to author, part 4.
9. gbaut5.idx - Index of the entries according to author, part 5.
10. gbaut6.idx - Index of the entries according to author, part 6.
11. gbaut7.idx - Index of the entries according to author, part 7.
12. gbaut8.idx - Index of the entries according to author, part 8.
13. gbaut9.idx - Index of the entries according to author, part 9.
14. gbaut10.idx - Index of the entries according to author, part 10.
15. gbaut11.idx - Index of the entries according to author, part 11.
16. gbaut12.idx - Index of the entries according to author, part 12.
17. gbaut13.idx - Index of the entries according to author, part 13.
18. gbaut14.idx - Index of the entries according to author, part 14.
19. gbaut15.idx - Index of the entries according to author, part 15.
20. gbaut16.idx - Index of the entries according to author, part 16.
21. gbaut17.idx - Index of the entries according to author, part 17.
22. gbaut18.idx - Index of the entries according to author, part 18.
23. gbaut19.idx - Index of the entries according to author, part 19.
24. gbjou.idx - Index of the entries according to journal citation.
25. gbgen.idx - Index of the entries according to gene names.
26. gbsec.idx - Index of the entries according to secondary accession number.
27. gbpri1.seq - Primate sequence entries, part 1.
28. gbpri2.seq - Primate sequence entries, part 2.
29. gbpri3.seq - Primate sequence entries, part 3.
30. gbpri4.seq - Primate sequence entries, part 4.
31. gbpri5.seq - Primate sequence entries, part 5.
32. gbpri6.seq - Primate sequence entries, part 6.
33. gbpri7.seq - Primate sequence entries, part 7.
34. gbpri8.seq - Primate sequence entries, part 8.
35. gbpri9.seq - Primate sequence entries, part 9.
36. gbpri10.seq - Primate sequence entries, part 10.
37. gbpri11.seq - Primate sequence entries, part 11.
38. gbpri12.seq - Primate sequence entries, part 12.
39. gbpri13.seq - Primate sequence entries, part 13.
40. gbpri14.seq - Primate sequence entries, part 14.
41. gbpri15.seq - Primate sequence entries, part 15.
42. gbpri16.seq - Primate sequence entries, part 16.
43. gbpri17.seq - Primate sequence entries, part 17.
44. gbpri18.seq - Primate sequence entries, part 18.
45. gbpri19.seq - Primate sequence entries, part 19.
46. gbpri20.seq - Primate sequence entries, part 20.
47. gbpri21.seq - Primate sequence entries, part 21.
48. gbpri22.seq - Primate sequence entries, part 22.
49. gbpri23.seq - Primate sequence entries, part 23.
50. gbpri24.seq - Primate sequence entries, part 24.
51. gbpri25.seq - Primate sequence entries, part 25.
52. gbrod1.seq - Rodent sequence entries, part 1.
53. gbrod2.seq - Rodent sequence entries, part 2.
54. gbrod3.seq - Rodent sequence entries, part 3.
55. gbrod4.seq - Rodent sequence entries, part 4.
56. gbrod5.seq - Rodent sequence entries, part 5.
57. gbrod6.seq - Rodent sequence entries, part 6.
58. gbrod7.seq - Rodent sequence entries, part 7.
59. gbmam.seq - Other mammalian sequence entries.
60. gbvrt1.seq - Other vertebrate sequence entries, part 1.
61. gbvrt2.seq - Other vertebrate sequence entries, part 2.
62. gbinv1.seq - Invertebrate sequence entries, part 1.
63. gbinv2.seq - Invertebrate sequence entries, part 2.
64. gbinv3.seq - Invertebrate sequence entries, part 3.
65. gbinv4.seq - Invertebrate sequence entries, part 4.
66. gbinv5.seq - Invertebrate sequence entries, part 5.
67. gbinv6.seq - Invertebrate sequence entries, part 6.
68. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
69. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
70. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
71. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
72. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
73. gbpln6.seq - Plant sequence entries (including fungi and algae), part 6.
74. gbpln7.seq - Plant sequence entries (including fungi and algae), part 7.
75. gbbct1.seq - Bacterial sequence entries, part 1.
76. gbbct2.seq - Bacterial sequence entries, part 2.
77. gbbct3.seq - Bacterial sequence entries, part 3.
78. gbbct4.seq - Bacterial sequence entries, part 4.
79. gbbct5.seq - Bacterial sequence entries, part 5.
80. gbbct6.seq - Bacterial sequence entries, part 6.
81. gbbct7.seq - Bacterial sequence entries, part 7.
82. gbvrl1.seq - Viral sequence entries, part 1.
83. gbvrl2.seq - Viral sequence entries, part 2.
84. gbvrl3.seq - Viral sequence entries, part 3.
85. gbphg.seq - Phage sequence entries.
86. gbsyn.seq - Synthetic and chimeric sequence entries.
87. gbuna.seq - Unannotated sequence entries.
88. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
89. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
90. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
91. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
92. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
93. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
94. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
95. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
96. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
97. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
98. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
99. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
100. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
101. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
102. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
103. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
104. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
105. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
106. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
107. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
108. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
109. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
110. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
111. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
112. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
113. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
114. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
115. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
116. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
117. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
118. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
119. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
120. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
121. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
122. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
123. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
124. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
125. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
126. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
127. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
128. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
129. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
130. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
131. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
132. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
133. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
134. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
135. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
136. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
137. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
138. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
139. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
140. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
141. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
142. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
143. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
144. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
145. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
146. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
147. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
148. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
149. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
150. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
151. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
152. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
153. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
154. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
155. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
156. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
157. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
158. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
159. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
160. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
161. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
162. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
163. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
164. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
165. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
166. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
167. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
168. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
169. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
170. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
171. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
172. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
173. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
174. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
175. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
176. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
177. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
178. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
179. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
180. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
181. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
182. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
183. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
184. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
185. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
186. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
187. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
188. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
189. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
190. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
191. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
192. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
193. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
194. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
195. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
196. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
197. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
198. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
199. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
200. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
201. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
202. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
203. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
204. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
205. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
206. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
207. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
208. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
209. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
210. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
211. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
212. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
213. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
214. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
215. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
216. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
217. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
218. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
219. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
220. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
221. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
222. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
223. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
224. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
225. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
226. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
227. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
228. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
229. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
230. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
231. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
232. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
233. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
234. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
235. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
236. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
237. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
238. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
239. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
240. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
241. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
242. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
243. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
244. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
245. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
246. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
247. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
248. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
249. gbest162.seq - EST (expressed sequence tag) sequence entries, part 162.
250. gbest163.seq - EST (expressed sequence tag) sequence entries, part 163.
251. gbest164.seq - EST (expressed sequence tag) sequence entries, part 164.
252. gbest165.seq - EST (expressed sequence tag) sequence entries, part 165.
253. gbest166.seq - EST (expressed sequence tag) sequence entries, part 166.
254. gbest167.seq - EST (expressed sequence tag) sequence entries, part 167.
255. gbest168.seq - EST (expressed sequence tag) sequence entries, part 168.
256. gbest169.seq - EST (expressed sequence tag) sequence entries, part 169.
257. gbest170.seq - EST (expressed sequence tag) sequence entries, part 170.
258. gbest171.seq - EST (expressed sequence tag) sequence entries, part 171.
259. gbest172.seq - EST (expressed sequence tag) sequence entries, part 172.
260. gbest173.seq - EST (expressed sequence tag) sequence entries, part 173.
261. gbest174.seq - EST (expressed sequence tag) sequence entries, part 174.
262. gbest175.seq - EST (expressed sequence tag) sequence entries, part 175.
263. gbest176.seq - EST (expressed sequence tag) sequence entries, part 176.
264. gbest177.seq - EST (expressed sequence tag) sequence entries, part 177.
265. gbest178.seq - EST (expressed sequence tag) sequence entries, part 178.
266. gbest179.seq - EST (expressed sequence tag) sequence entries, part 179.
267. gbest180.seq - EST (expressed sequence tag) sequence entries, part 180.
268. gbest181.seq - EST (expressed sequence tag) sequence entries, part 181.
269. gbest182.seq - EST (expressed sequence tag) sequence entries, part 182.
270. gbest183.seq - EST (expressed sequence tag) sequence entries, part 183.
271. gbest184.seq - EST (expressed sequence tag) sequence entries, part 184.
272. gbest185.seq - EST (expressed sequence tag) sequence entries, part 185.
273. gbest186.seq - EST (expressed sequence tag) sequence entries, part 186.
274. gbest187.seq - EST (expressed sequence tag) sequence entries, part 187.
275. gbest188.seq - EST (expressed sequence tag) sequence entries, part 188.
276. gbest189.seq - EST (expressed sequence tag) sequence entries, part 189.
277. gbest190.seq - EST (expressed sequence tag) sequence entries, part 190.
278. gbest191.seq - EST (expressed sequence tag) sequence entries, part 191.
279. gbest192.seq - EST (expressed sequence tag) sequence entries, part 192.
280. gbest193.seq - EST (expressed sequence tag) sequence entries, part 193.
281. gbest194.seq - EST (expressed sequence tag) sequence entries, part 194.
282. gbest195.seq - EST (expressed sequence tag) sequence entries, part 195.
283. gbest196.seq - EST (expressed sequence tag) sequence entries, part 196.
284. gbest197.seq - EST (expressed sequence tag) sequence entries, part 197.
285. gbest198.seq - EST (expressed sequence tag) sequence entries, part 198.
286. gbest199.seq - EST (expressed sequence tag) sequence entries, part 199.
287. gbest200.seq - EST (expressed sequence tag) sequence entries, part 200.
288. gbest201.seq - EST (expressed sequence tag) sequence entries, part 201.
289. gbest202.seq - EST (expressed sequence tag) sequence entries, part 202.
290. gbest203.seq - EST (expressed sequence tag) sequence entries, part 203.
291. gbest204.seq - EST (expressed sequence tag) sequence entries, part 204.
292. gbest205.seq - EST (expressed sequence tag) sequence entries, part 205.
293. gbest206.seq - EST (expressed sequence tag) sequence entries, part 206.
294. gbest207.seq - EST (expressed sequence tag) sequence entries, part 207.
295. gbest208.seq - EST (expressed sequence tag) sequence entries, part 208.
296. gbest209.seq - EST (expressed sequence tag) sequence entries, part 209.
297. gbest210.seq - EST (expressed sequence tag) sequence entries, part 210.
298. gbest211.seq - EST (expressed sequence tag) sequence entries, part 211.
299. gbest212.seq - EST (expressed sequence tag) sequence entries, part 212.
300. gbest213.seq - EST (expressed sequence tag) sequence entries, part 213.
301. gbest214.seq - EST (expressed sequence tag) sequence entries, part 214.
302. gbest215.seq - EST (expressed sequence tag) sequence entries, part 215.
303. gbest216.seq - EST (expressed sequence tag) sequence entries, part 216.
304. gbest217.seq - EST (expressed sequence tag) sequence entries, part 217.
305. gbest218.seq - EST (expressed sequence tag) sequence entries, part 218.
306. gbest219.seq - EST (expressed sequence tag) sequence entries, part 219.
307. gbest220.seq - EST (expressed sequence tag) sequence entries, part 220.
308. gbest221.seq - EST (expressed sequence tag) sequence entries, part 221.
309. gbest222.seq - EST (expressed sequence tag) sequence entries, part 222.
310. gbest223.seq - EST (expressed sequence tag) sequence entries, part 223.
311. gbest224.seq - EST (expressed sequence tag) sequence entries, part 224.
312. gbest225.seq - EST (expressed sequence tag) sequence entries, part 225.
313. gbest226.seq - EST (expressed sequence tag) sequence entries, part 226.
314. gbest227.seq - EST (expressed sequence tag) sequence entries, part 227.
315. gbest228.seq - EST (expressed sequence tag) sequence entries, part 228.
316. gbest229.seq - EST (expressed sequence tag) sequence entries, part 229.
317. gbest230.seq - EST (expressed sequence tag) sequence entries, part 230.
318. gbest231.seq - EST (expressed sequence tag) sequence entries, part 231.
319. gbest232.seq - EST (expressed sequence tag) sequence entries, part 232.
320. gbest233.seq - EST (expressed sequence tag) sequence entries, part 233.
321. gbest234.seq - EST (expressed sequence tag) sequence entries, part 234.
322. gbest235.seq - EST (expressed sequence tag) sequence entries, part 235.
323. gbest236.seq - EST (expressed sequence tag) sequence entries, part 236.
324. gbest237.seq - EST (expressed sequence tag) sequence entries, part 237.
325. gbest238.seq - EST (expressed sequence tag) sequence entries, part 238.
326. gbest239.seq - EST (expressed sequence tag) sequence entries, part 239.
327. gbest240.seq - EST (expressed sequence tag) sequence entries, part 240.
328. gbest241.seq - EST (expressed sequence tag) sequence entries, part 241.
329. gbest242.seq - EST (expressed sequence tag) sequence entries, part 242.
330. gbest243.seq - EST (expressed sequence tag) sequence entries, part 243.
331. gbest244.seq - EST (expressed sequence tag) sequence entries, part 244.
332. gbpat1.seq - Patent sequence entries, part 1.
333. gbpat2.seq - Patent sequence entries, part 2.
334. gbpat3.seq - Patent sequence entries, part 3.
335. gbpat4.seq - Patent sequence entries, part 4.
336. gbpat5.seq - Patent sequence entries, part 5.
337. gbpat6.seq - Patent sequence entries, part 6.
338. gbpat7.seq - Patent sequence entries, part 7.
339. gbpat8.seq - Patent sequence entries, part 8.
340. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
341. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
342. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
343. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
344. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
345. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
346. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
347. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
348. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
349. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
350. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
351. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
352. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
353. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
354. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
355. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
356. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
357. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
358. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
359. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
360. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
361. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
362. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
363. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
364. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
365. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
366. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
367. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
368. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
369. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
370. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
371. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
372. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
373. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
374. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
375. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
376. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
377. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
378. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
379. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
380. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
381. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
382. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
383. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
384. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
385. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
386. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
387. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
388. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
389. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
390. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
391. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
392. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
393. gbgss52.seq - GSS (genome survey sequence) sequence entries, part 52.
394. gbgss53.seq - GSS (genome survey sequence) sequence entries, part 53.
395. gbgss54.seq - GSS (genome survey sequence) sequence entries, part 54.
396. gbgss55.seq - GSS (genome survey sequence) sequence entries, part 55.
397. gbgss56.seq - GSS (genome survey sequence) sequence entries, part 56.
398. gbgss57.seq - GSS (genome survey sequence) sequence entries, part 57.
399. gbgss58.seq - GSS (genome survey sequence) sequence entries, part 58.
400. gbgss59.seq - GSS (genome survey sequence) sequence entries, part 59.
401. gbgss60.seq - GSS (genome survey sequence) sequence entries, part 60.
402. gbgss61.seq - GSS (genome survey sequence) sequence entries, part 61.
403. gbgss62.seq - GSS (genome survey sequence) sequence entries, part 62.
404. gbgss63.seq - GSS (genome survey sequence) sequence entries, part 63.
405. gbgss64.seq - GSS (genome survey sequence) sequence entries, part 64.
406. gbgss65.seq - GSS (genome survey sequence) sequence entries, part 65.
407. gbgss66.seq - GSS (genome survey sequence) sequence entries, part 66.
408. gbgss67.seq - GSS (genome survey sequence) sequence entries, part 67.
409. gbgss68.seq - GSS (genome survey sequence) sequence entries, part 68.
410. gbgss69.seq - GSS (genome survey sequence) sequence entries, part 69.
411. gbgss70.seq - GSS (genome survey sequence) sequence entries, part 70.
412. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
413. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
414. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
415. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
416. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
417. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
418. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
419. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
420. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
421. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
422. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
423. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
424. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
425. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
426. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
427. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
428. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
429. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
430. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
431. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
432. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
433. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
434. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
435. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
436. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
437. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
438. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
439. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
440. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
441. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
442. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
443. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
444. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
445. gbhtg34.seq - HTGS (high throughput genomic sequencing) sequence entries, part 34.
446. gbhtg35.seq - HTGS (high throughput genomic sequencing) sequence entries, part 35.
447. gbhtg36.seq - HTGS (high throughput genomic sequencing) sequence entries, part 36.
448. gbhtg37.seq - HTGS (high throughput genomic sequencing) sequence entries, part 37.
449. gbhtg38.seq - HTGS (high throughput genomic sequencing) sequence entries, part 38.
450. gbhtg39.seq - HTGS (high throughput genomic sequencing) sequence entries, part 39.
451. gbhtg40.seq - HTGS (high throughput genomic sequencing) sequence entries, part 40.
452. gbhtg41.seq - HTGS (high throughput genomic sequencing) sequence entries, part 41.
453. gbhtg42.seq - HTGS (high throughput genomic sequencing) sequence entries, part 42.
454. gbhtg43.seq - HTGS (high throughput genomic sequencing) sequence entries, part 43.
455. gbhtg44.seq - HTGS (high throughput genomic sequencing) sequence entries, part 44.
456. gbhtg45.seq - HTGS (high throughput genomic sequencing) sequence entries, part 45.
457. gbhtg46.seq - HTGS (high throughput genomic sequencing) sequence entries, part 46.
458. gbhtg47.seq - HTGS (high throughput genomic sequencing) sequence entries, part 47.
459. gbhtg48.seq - HTGS (high throughput genomic sequencing) sequence entries, part 48.
460. gbhtg49.seq - HTGS (high throughput genomic sequencing) sequence entries, part 49.
461. gbhtg50.seq - HTGS (high throughput genomic sequencing) sequence entries, part 50.
462. gbhtg51.seq - HTGS (high throughput genomic sequencing) sequence entries, part 51.
463. gbhtg52.seq - HTGS (high throughput genomic sequencing) sequence entries, part 52.
464. gbhtg53.seq - HTGS (high throughput genomic sequencing) sequence entries, part 53.
465. gbhtg54.seq - HTGS (high throughput genomic sequencing) sequence entries, part 54.
466. gbhtg55.seq - HTGS (high throughput genomic sequencing) sequence entries, part 55.
467. gbhtg56.seq - HTGS (high throughput genomic sequencing) sequence entries, part 56.
468. gbhtg57.seq - HTGS (high throughput genomic sequencing) sequence entries, part 57.
469. gbhtg58.seq - HTGS (high throughput genomic sequencing) sequence entries, part 58.
470. gbhtg59.seq - HTGS (high throughput genomic sequencing) sequence entries, part 59.
471. gbhtg60.seq - HTGS (high throughput genomic sequencing) sequence entries, part 60.
472. gbhtg61.seq - HTGS (high throughput genomic sequencing) sequence entries, part 61.
473. gbhtg62.seq - HTGS (high throughput genomic sequencing) sequence entries, part 62.
474. gbhtc1.seq - HTC (high throughput cDNA sequencing) entries, part 1.
475. gbhtc2.seq - HTC (high throughput cDNA sequencing) entries, part 2.
476. gbhtc3.seq - HTC (high throughput cDNA sequencing) entries, part 3.
477. gbhtc4.seq - HTC (high throughput cDNA sequencing) entries, part 4.
478. gbcon.seq - CON division entries (see description below for details)
479. gbchg.txt - Accession numbers of entries updated since the previous release.
480. gbdel.txt - Accession numbers of entries deleted since the previous release.
481. gbnew.txt - Accession numbers of entries new since the previous release.
The gbcon.seq data file provides an alternative representation for complex
sequences, such as segmented sets and complete-genomes that have been split
into pieces. These "CON" records do not contain sequence data; they utilize
a CONTIG linetype with a join() statement which describes how the component
sequences can be assembled to form the larger sequence. The contents of the
CON division are not reflected in the 'index' files that accompany GenBank
releases. The GenBank README describes the CON division of GenBank in more
detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 135.0 flatfiles require roughly 100 GB (sequence
files only) or 114 GB (including the 'short directory' and 'index' files).
The following table contains the approximate sizes of the individual files in
this release. Since minor changes to some of the files might have occurred
after these release notes were written, these sizes should not be used to
determine file integrity; they are provided as an aid to planning only.
File Size File Name
250008056 gbbct1.seq
250340813 gbbct2.seq
250000317 gbbct3.seq
250111246 gbbct4.seq
250007321 gbbct5.seq
250002635 gbbct6.seq
52586799 gbbct7.seq
4903037 gbchg.txt
357869 gbdel.txt
230687980 gbest1.seq
230688724 gbest10.seq
230688834 gbest100.seq
230691114 gbest101.seq
230689970 gbest102.seq
230689348 gbest103.seq
230689697 gbest104.seq
230690100 gbest105.seq
230689984 gbest106.seq
230688549 gbest107.seq
230689245 gbest108.seq
230689805 gbest109.seq
230689156 gbest11.seq
230689606 gbest110.seq
230690293 gbest111.seq
230689413 gbest112.seq
230690499 gbest113.seq
230688130 gbest114.seq
230688562 gbest115.seq
230687843 gbest116.seq
230687655 gbest117.seq
230688453 gbest118.seq
230689264 gbest119.seq
230690674 gbest12.seq
230689725 gbest120.seq
230687475 gbest121.seq
230687880 gbest122.seq
230690252 gbest123.seq
230689718 gbest124.seq
230688282 gbest125.seq
230688955 gbest126.seq
230689752 gbest127.seq
230689280 gbest128.seq
230688721 gbest129.seq
230689435 gbest13.seq
230688811 gbest130.seq
230689562 gbest131.seq
230687881 gbest132.seq
230689053 gbest133.seq
230690568 gbest134.seq
230689247 gbest135.seq
230689633 gbest136.seq
230688628 gbest137.seq
230687991 gbest138.seq
230688879 gbest139.seq
230688790 gbest14.seq
230687724 gbest140.seq
230689607 gbest141.seq
230688007 gbest142.seq
230689973 gbest143.seq
230690066 gbest144.seq
230688783 gbest145.seq
230687636 gbest146.seq
230690183 gbest147.seq
230688367 gbest148.seq
230687938 gbest149.seq
230688941 gbest15.seq
230689420 gbest150.seq
230688553 gbest151.seq
230687779 gbest152.seq
230691636 gbest153.seq
230690442 gbest154.seq
230691455 gbest155.seq
230688374 gbest156.seq
230689564 gbest157.seq
230689916 gbest158.seq
230688646 gbest159.seq
230688299 gbest16.seq
230688766 gbest160.seq
230688193 gbest161.seq
230690130 gbest162.seq
230690541 gbest163.seq
230687560 gbest164.seq
230688990 gbest165.seq
230690672 gbest166.seq
230687965 gbest167.seq
230688567 gbest168.seq
230688459 gbest169.seq
230688340 gbest17.seq
230688629 gbest170.seq
230688586 gbest171.seq
230687578 gbest172.seq
230690109 gbest173.seq
230687856 gbest174.seq
230687938 gbest175.seq
230689271 gbest176.seq
230687820 gbest177.seq
230688363 gbest178.seq
230690605 gbest179.seq
230689704 gbest18.seq
230688098 gbest180.seq
230689571 gbest181.seq
230688483 gbest182.seq
230688219 gbest183.seq
230687792 gbest184.seq
230689098 gbest185.seq
230688559 gbest186.seq
230688341 gbest187.seq
230688599 gbest188.seq
230687832 gbest189.seq
230689392 gbest19.seq
191433811 gbest190.seq
163448723 gbest191.seq
164567180 gbest192.seq
171931572 gbest193.seq
170683582 gbest194.seq
164553449 gbest195.seq
165967786 gbest196.seq
165531023 gbest197.seq
164870634 gbest198.seq
165556914 gbest199.seq
230690391 gbest2.seq
230690492 gbest20.seq
164988392 gbest200.seq
165035087 gbest201.seq
163782348 gbest202.seq
168623572 gbest203.seq
163246448 gbest204.seq
163922226 gbest205.seq
168111044 gbest206.seq
168555718 gbest207.seq
166623004 gbest208.seq
166479462 gbest209.seq
230687476 gbest21.seq
166039120 gbest210.seq
165994062 gbest211.seq
165158556 gbest212.seq
165110187 gbest213.seq
165948878 gbest214.seq
165861414 gbest215.seq
181088202 gbest216.seq
173196948 gbest217.seq
215894609 gbest218.seq
230689023 gbest219.seq
230688023 gbest22.seq
230688338 gbest220.seq
230690321 gbest221.seq
230687675 gbest222.seq
230691397 gbest223.seq
230689123 gbest224.seq
230688435 gbest225.seq
230687461 gbest226.seq
230687945 gbest227.seq
230690529 gbest228.seq
230688056 gbest229.seq
230689663 gbest23.seq
230688700 gbest230.seq
230687654 gbest231.seq
230690333 gbest232.seq
230688582 gbest233.seq
230687984 gbest234.seq
230687641 gbest235.seq
230688761 gbest236.seq
230688639 gbest237.seq
230688394 gbest238.seq
230690387 gbest239.seq
230689145 gbest24.seq
230688319 gbest240.seq
230690464 gbest241.seq
223247528 gbest242.seq
230688661 gbest243.seq
229580597 gbest244.seq
230691318 gbest25.seq
230690532 gbest26.seq
230689185 gbest27.seq
230689325 gbest28.seq
230687613 gbest29.seq
230688556 gbest3.seq
230689038 gbest30.seq
230687592 gbest31.seq
230689040 gbest32.seq
230688498 gbest33.seq
230688872 gbest34.seq
230688173 gbest35.seq
191812762 gbest36.seq
191089106 gbest37.seq
205972256 gbest38.seq
215947882 gbest39.seq
230689876 gbest4.seq
216529116 gbest40.seq
216975664 gbest41.seq
221949848 gbest42.seq
230688503 gbest43.seq
230689313 gbest44.seq
216817561 gbest45.seq
230688873 gbest46.seq
230688153 gbest47.seq
230689655 gbest48.seq
230691777 gbest49.seq
165267638 gbest5.seq
230688477 gbest50.seq
230687696 gbest51.seq
230688647 gbest52.seq
230690130 gbest53.seq
230689588 gbest54.seq
230690287 gbest55.seq
230689911 gbest56.seq
230689920 gbest57.seq
230689464 gbest58.seq
230687854 gbest59.seq
180014575 gbest6.seq
230689102 gbest60.seq
218210323 gbest61.seq
209529812 gbest62.seq
209166704 gbest63.seq
209116506 gbest64.seq
209541016 gbest65.seq
210927787 gbest66.seq
209389084 gbest67.seq
208918686 gbest68.seq
210179833 gbest69.seq
230687546 gbest7.seq
210098112 gbest70.seq
205398071 gbest71.seq
207796243 gbest72.seq
207271031 gbest73.seq
209610222 gbest74.seq
220526657 gbest75.seq
230691233 gbest76.seq
230688461 gbest77.seq
225719625 gbest78.seq
215561750 gbest79.seq
230689635 gbest8.seq
213300610 gbest80.seq
224032226 gbest81.seq
230687440 gbest82.seq
230689909 gbest83.seq
230687795 gbest84.seq
230689919 gbest85.seq
230687868 gbest86.seq
230687947 gbest87.seq
230689172 gbest88.seq
230689256 gbest89.seq
230687906 gbest9.seq
230689805 gbest90.seq
230688011 gbest91.seq
230689395 gbest92.seq
230688880 gbest93.seq
230688128 gbest94.seq
230688324 gbest95.seq
230688363 gbest96.seq
230689085 gbest97.seq
230689376 gbest98.seq
230688059 gbest99.seq
209716920 gbgss1.seq
209718305 gbgss10.seq
209718180 gbgss11.seq
209718416 gbgss12.seq
209716260 gbgss13.seq
209718883 gbgss14.seq
209717939 gbgss15.seq
209718767 gbgss16.seq
209717105 gbgss17.seq
209718096 gbgss18.seq
209718985 gbgss19.seq
209717675 gbgss2.seq
209716935 gbgss20.seq
209718576 gbgss21.seq
209719322 gbgss22.seq
209717966 gbgss23.seq
209719408 gbgss24.seq
209718651 gbgss25.seq
209717323 gbgss26.seq
209719456 gbgss27.seq
209716929 gbgss28.seq
209716350 gbgss29.seq
209717368 gbgss3.seq
209717310 gbgss30.seq
209716764 gbgss31.seq
209716465 gbgss32.seq
209718307 gbgss33.seq
209717120 gbgss34.seq
209715977 gbgss35.seq
209716452 gbgss36.seq
209717134 gbgss37.seq
209716195 gbgss38.seq
209717139 gbgss39.seq
209717202 gbgss4.seq
209717500 gbgss40.seq
209716726 gbgss41.seq
209716891 gbgss42.seq
209716980 gbgss43.seq
209715984 gbgss44.seq
209717174 gbgss45.seq
209716335 gbgss46.seq
209718511 gbgss47.seq
209718210 gbgss48.seq
209718668 gbgss49.seq
209716600 gbgss5.seq
209717723 gbgss50.seq
209718035 gbgss51.seq
209716598 gbgss52.seq
209716385 gbgss53.seq
209718139 gbgss54.seq
209719027 gbgss55.seq
209718087 gbgss56.seq
209718163 gbgss57.seq
209717248 gbgss58.seq
16761637 gbgss59.seq
209717310 gbgss6.seq
250000979 gbgss60.seq
250001658 gbgss61.seq
250002510 gbgss62.seq
250000468 gbgss63.seq
250001469 gbgss64.seq
250002608 gbgss65.seq
250001001 gbgss66.seq
250002188 gbgss67.seq
250002151 gbgss68.seq
250000376 gbgss69.seq
209716294 gbgss7.seq
108296036 gbgss70.seq
209716634 gbgss8.seq
209717702 gbgss9.seq
250002972 gbhtc1.seq
250000035 gbhtc2.seq
250000047 gbhtc3.seq
72810660 gbhtc4.seq
250124391 gbhtg1.seq
250141702 gbhtg10.seq
250065160 gbhtg11.seq
250151996 gbhtg12.seq
250284315 gbhtg13.seq
250008859 gbhtg14.seq
250228689 gbhtg15.seq
250183613 gbhtg16.seq
250181730 gbhtg17.seq
250003050 gbhtg18.seq
250063265 gbhtg19.seq
250002252 gbhtg2.seq
250230970 gbhtg20.seq
250102694 gbhtg21.seq
250006157 gbhtg22.seq
250165240 gbhtg23.seq
250036162 gbhtg24.seq
250553067 gbhtg25.seq
250023408 gbhtg26.seq
250165358 gbhtg27.seq
250032145 gbhtg28.seq
250074856 gbhtg29.seq
250057937 gbhtg3.seq
250179734 gbhtg30.seq
250175261 gbhtg31.seq
250141745 gbhtg32.seq
250149622 gbhtg33.seq
250030598 gbhtg34.seq
250182563 gbhtg35.seq
250244624 gbhtg36.seq
250094833 gbhtg37.seq
250140012 gbhtg38.seq
250258326 gbhtg39.seq
250150481 gbhtg4.seq
250124017 gbhtg40.seq
250215295 gbhtg41.seq
250002642 gbhtg42.seq
250292435 gbhtg43.seq
250193221 gbhtg44.seq
250135232 gbhtg45.seq
250171894 gbhtg46.seq
250020468 gbhtg47.seq
250057780 gbhtg48.seq
250098248 gbhtg49.seq
250064896 gbhtg5.seq
250081386 gbhtg50.seq
250056005 gbhtg51.seq
250058498 gbhtg52.seq
250109054 gbhtg53.seq
250085158 gbhtg54.seq
250067711 gbhtg55.seq
250348527 gbhtg56.seq
250059651 gbhtg57.seq
250140895 gbhtg58.seq
250059656 gbhtg59.seq
250080913 gbhtg6.seq
250108995 gbhtg60.seq
250019908 gbhtg61.seq
89591466 gbhtg62.seq
250006267 gbhtg7.seq
250112106 gbhtg8.seq
250013149 gbhtg9.seq
250118265 gbinv1.seq
250058820 gbinv2.seq
250001766 gbinv3.seq
250051421 gbinv4.seq
250028832 gbinv5.seq
33388884 gbinv6.seq
166599068 gbmam.seq
15573259 gbnew.txt
250000479 gbpat1.seq
250000822 gbpat2.seq
250002364 gbpat3.seq
250016754 gbpat4.seq
250000057 gbpat5.seq
250001224 gbpat6.seq
250002785 gbpat7.seq
112395004 gbpat8.seq
22016571 gbphg.seq
250098284 gbpln1.seq
250006718 gbpln2.seq
250190187 gbpln3.seq
250000425 gbpln4.seq
250001062 gbpln5.seq
250032263 gbpln6.seq
209839114 gbpln7.seq
250019676 gbpri1.seq
250008409 gbpri10.seq
250205171 gbpri11.seq
250090001 gbpri12.seq
250149375 gbpri13.seq
250002403 gbpri14.seq
250004010 gbpri15.seq
250102107 gbpri16.seq
250056188 gbpri17.seq
250138643 gbpri18.seq
250055086 gbpri19.seq
250064176 gbpri2.seq
250128242 gbpri20.seq
250116704 gbpri21.seq
250032041 gbpri22.seq
250013553 gbpri23.seq
250262780 gbpri24.seq
115285980 gbpri25.seq
250083502 gbpri3.seq
250157986 gbpri4.seq
250016248 gbpri5.seq
250014484 gbpri6.seq
250017374 gbpri7.seq
250059972 gbpri8.seq
250091367 gbpri9.seq
142707 gbrel.txt
250157970 gbrod1.seq
250085714 gbrod2.seq
250059797 gbrod3.seq
250148885 gbrod4.seq
250121964 gbrod5.seq
250001760 gbrod6.seq
152079323 gbrod7.seq
250002424 gbsts1.seq
198997531 gbsts2.seq
37558160 gbsyn.seq
1460672 gbuna.seq
250001283 gbvrl1.seq
250002104 gbvrl2.seq
123204942 gbvrl3.seq
250123896 gbvrt1.seq
245211320 gbvrt2.seq
2.2.6 Per-Division Statistics
The following table provides a per-division breakdown of the number of
sequence entries and the total number of bases of DNA/RNA in each sequence
data file:
Division Entries Bases
BCT1 22333 100379900
BCT2 7912 106754176
BCT3 43282 96867044
BCT4 25641 101694411
BCT5 37466 99285347
BCT6 35845 92360953
BCT7 13486 17559924
EST1 68333 26365039
EST10 76750 29944017
EST100 70063 31222696
EST101 65277 31138029
EST102 67351 40481514
EST103 70672 36450075
EST104 70191 45696781
EST105 76103 34426431
EST106 74362 27724701
EST107 75786 25968266
EST108 73394 40792331
EST109 66623 33337644
EST11 75354 28760075
EST110 78892 49350961
EST111 79316 44995238
EST112 72700 45605089
EST113 68975 42444999
EST114 73299 47384282
EST115 68278 44960894
EST116 73456 43946000
EST117 76527 44197686
EST118 72439 49405137
EST119 75716 47698272
EST12 77467 30841318
EST120 73373 47512164
EST121 78428 36186422
EST122 78346 27288568
EST123 80572 49697914
EST124 74893 43050898
EST125 65498 36403756
EST126 72155 36267101
EST127 69600 38481761
EST128 65965 36817825
EST129 71814 43228688
EST13 77187 29183542
EST130 72968 46338306
EST131 68427 39655545
EST132 70371 39606843
EST133 73314 45077870
EST134 67491 39619485
EST135 65580 37464253
EST136 102964 56009823
EST137 81820 46243063
EST138 101801 53323100
EST139 108818 58205102
EST14 78676 31968060
EST140 101801 56059723
EST141 89643 53833035
EST142 69178 37280286
EST143 65948 30643643
EST144 60869 29919648
EST145 57658 29951648
EST146 62507 31024495
EST147 59109 30563636
EST148 78748 56458394
EST149 67646 38794225
EST15 73885 31230008
EST150 75648 49305337
EST151 68085 37456644
EST152 62226 30818734
EST153 64993 40675939
EST154 67867 30684074
EST155 63160 47417204
EST156 76104 41783523
EST157 71885 40027107
EST158 68138 45144724
EST159 65874 37780165
EST16 75563 33234361
EST160 63704 41859132
EST161 67431 31741434
EST162 75467 29693373
EST163 71539 45473602
EST164 82134 41165759
EST165 62111 32362038
EST166 68230 49204021
EST167 71526 46666704
EST168 67954 36367439
EST169 68476 44991962
EST17 83217 34228100
EST170 69770 53931519
EST171 69220 34421854
EST172 71227 41330738
EST173 70290 60296923
EST174 65493 48595950
EST175 63958 46570344
EST176 63481 47053321
EST177 65482 45589182
EST178 65595 48061430
EST179 63644 45749572
EST18 80507 32237375
EST180 64596 39500044
EST181 62701 34191442
EST182 67971 39351891
EST183 82993 48657386
EST184 83390 53972780
EST185 78375 45816507
EST186 105796 65713044
EST187 108123 64812782
EST188 99505 59625124
EST189 69435 37888053
EST19 78796 32293616
EST190 40271 19358255
EST191 27860 10582084
EST192 27672 10253223
EST193 26412 9739040
EST194 26678 8983970
EST195 27669 9946248
EST196 27261 10001350
EST197 27245 9815677
EST198 27384 10345436
EST199 27172 12118608
EST2 75036 28805559
EST20 74368 30186297
EST200 27287 11193785
EST201 27392 10145555
EST202 27680 9285897
EST203 26976 9296738
EST204 27863 11338385
EST205 27804 10844139
EST206 27086 11348178
EST207 26712 12020535
EST208 27135 11328113
EST209 27101 10945536
EST21 73749 34287531
EST210 27093 11591614
EST211 27206 11602031
EST212 27329 11054544
EST213 27324 10868382
EST214 27233 10510588
EST215 27238 11160279
EST216 24526 17461906
EST217 25815 17233488
EST218 81219 31364758
EST219 85966 42881866
EST22 75824 30423198
EST220 72576 42858452
EST221 72587 41928617
EST222 70409 44682463
EST223 55310 27912500
EST224 98776 46977528
EST225 90511 45058905
EST226 71613 39628711
EST227 61273 29293818
EST228 70415 45287613
EST229 71045 34667679
EST23 77270 32345060
EST230 71724 33811145
EST231 73987 45511274
EST232 66111 36836473
EST233 66577 37847961
EST234 85856 45930014
EST235 77786 50665830
EST236 80058 55071683
EST237 98488 40384720
EST238 73291 25848355
EST239 72350 27042723
EST24 75385 33684371
EST240 73972 26211122
EST241 72636 26425416
EST242 78094 26207206
EST243 72337 28984028
EST244 74156 28176770
EST25 72379 30761803
EST26 76165 31651139
EST27 76210 33159444
EST28 104259 49734558
EST29 70990 45436631
EST3 73894 29981502
EST30 82000 56531033
EST31 90879 50643389
EST32 97521 50049068
EST33 99778 46079263
EST34 95035 50555952
EST35 103423 46131628
EST36 69085 19025824
EST37 69388 18420507
EST38 74372 21983801
EST39 43538 12009316
EST4 74402 28251763
EST40 43391 11946196
EST41 43040 11967223
EST42 50932 16209680
EST43 99964 43647940
EST44 94488 45006618
EST45 86206 46047045
EST46 92911 44244538
EST47 107325 56054212
EST48 78955 35986472
EST49 68863 29030635
EST5 48500 15380287
EST50 71707 31952746
EST51 75520 32676575
EST52 73873 30659479
EST53 82308 32220677
EST54 68647 27387220
EST55 63814 29842604
EST56 72636 31854506
EST57 80753 36607612
EST58 74246 30116675
EST59 74268 26321444
EST6 55669 17851521
EST60 87745 40554255
EST61 49655 16543240
EST62 40176 11125416
EST63 40204 11992963
EST64 40509 12496194
EST65 40607 12198024
EST66 40518 13008206
EST67 40580 12683693
EST68 40447 12302944
EST69 40153 12110716
EST7 74567 29348606
EST70 40610 12668216
EST71 41477 11835124
EST72 41250 13071384
EST73 41117 12677221
EST74 41011 13503326
EST75 45674 11905851
EST76 40471 24798195
EST77 41995 22131068
EST78 45822 18797714
EST79 50270 23035829
EST8 76202 30681145
EST80 51819 21556377
EST81 57588 23409206
EST82 75864 31675794
EST83 74750 29041273
EST84 73343 34385606
EST85 77673 45950556
EST86 77228 42669158
EST87 76837 37513300
EST88 76106 41724506
EST89 73098 39640707
EST9 77738 29969805
EST90 72943 30234255
EST91 75180 45574367
EST92 70590 31132813
EST93 77558 49499043
EST94 64264 35081498
EST95 72451 37193672
EST96 74343 44323322
EST97 72569 43396630
EST98 70492 44691475
EST99 74522 36973407
GSS1 83259 35671986
GSS10 66628 34170373
GSS11 68874 40613204
GSS12 62891 31915338
GSS13 65649 34594000
GSS14 69181 36065538
GSS15 65586 29706266
GSS16 64442 29751507
GSS17 71555 41774784
GSS18 65568 33869929
GSS19 60253 27409644
GSS2 83485 35628036
GSS20 52118 27255184
GSS21 52560 26104499
GSS22 53721 23101999
GSS23 57869 33395282
GSS24 58810 30362788
GSS25 52942 25072120
GSS26 60553 39584091
GSS27 64361 27364590
GSS28 54058 22159080
GSS29 55495 27570609
GSS3 81437 38313330
GSS30 66668 31559765
GSS31 55462 32005282
GSS32 85583 38052236
GSS33 69621 36861469
GSS34 67978 38945146
GSS35 64911 41653666
GSS36 73306 35913834
GSS37 70019 37052179
GSS38 67635 36639416
GSS39 85256 54646391
GSS4 74355 38120558
GSS40 85995 57123944
GSS41 80834 42046824
GSS42 85181 52318952
GSS43 77824 34174761
GSS44 77331 30687246
GSS45 74851 46055788
GSS46 74201 52268656
GSS47 69531 48870543
GSS48 66294 43818220
GSS49 66360 43684541
GSS5 71182 38065436
GSS50 72178 40493541
GSS51 73077 37023900
GSS52 81289 57701455
GSS53 79819 66406853
GSS54 79829 41307110
GSS55 84935 58504603
GSS56 79167 51018141
GSS57 72162 41591439
GSS58 79450 43457520
GSS59 6084 2435610
GSS6 70655 35417193
GSS60 86691 65546719
GSS61 83144 62398056
GSS62 94492 38467829
GSS63 103974 64719062
GSS64 88625 60057904
GSS65 74792 62886396
GSS66 68469 57585778
GSS67 67401 62212096
GSS68 61202 54021370
GSS69 110004 55352772
GSS7 70944 35613266
GSS70 41086 18152298
GSS8 71352 36474319
GSS9 68975 34298886
HTC1 27550 44219507
HTC2 25838 58501740
HTC3 66330 73945617
HTC4 31885 22491529
HTG1 1329 190561958
HTG10 1239 189247603
HTG11 1413 187222495
HTG12 994 192046733
HTG13 722 192719814
HTG14 738 192465762
HTG15 723 192603914
HTG16 805 192471494
HTG17 729 192657210
HTG18 867 191686414
HTG19 2079 178750986
HTG2 2494 188144720
HTG20 1059 189721649
HTG21 1181 188660002
HTG22 903 191238336
HTG23 752 192440707
HTG24 963 190774836
HTG25 905 191750769
HTG26 920 191138097
HTG27 826 191787563
HTG28 773 192299915
HTG29 933 191202902
HTG3 2504 187892959
HTG30 866 191715177
HTG31 927 191432563
HTG32 1004 190655977
HTG33 979 190719240
HTG34 977 191014631
HTG35 1013 190626480
HTG36 918 191509014
HTG37 908 192395134
HTG38 1018 190930340
HTG39 943 192002373
HTG4 2570 189889508
HTG40 894 191853261
HTG41 867 192331437
HTG42 840 191878678
HTG43 890 191903599
HTG44 972 191315367
HTG45 967 191497999
HTG46 938 192158265
HTG47 958 191479938
HTG48 1075 190800245
HTG49 1190 189644719
HTG5 1296 188216184
HTG50 1126 190598194
HTG51 1351 189671122
HTG52 1099 191307454
HTG53 1165 190275138
HTG54 1137 190363857
HTG55 1145 191466402
HTG56 1225 191536275
HTG57 1011 193948708
HTG58 1141 191100457
HTG59 1386 194434732
HTG6 1290 187827583
HTG60 1034 194136240
HTG61 1179 192771655
HTG62 373 65747245
HTG7 1251 188040761
HTG8 1280 187774738
HTG9 1208 189224660
INV1 9894 173210990
INV2 1927 165627815
INV3 56390 92509317
INV4 56930 88995664
INV5 37712 107899276
INV6 1446 18433034
MAM 48388 56598112
PAT1 220705 69299651
PAT2 166181 92230177
PAT3 150201 81059309
PAT4 104780 117483058
PAT5 138657 90596286
PAT6 118997 63842585
PAT7 100147 62130981
PAT8 91308 27343708
PHG 2308 8408961
PLN1 20254 138902720
PLN2 62697 97954505
PLN3 58090 96218538
PLN4 19182 134222345
PLN5 59663 70734510
PLN6 50283 100661503
PLN7 36022 88559465
PRI1 13921 154817943
PRI10 1386 174020684
PRI11 1270 175465712
PRI12 1512 175127330
PRI13 1608 178651625
PRI14 19711 154040823
PRI15 43879 112245457
PRI16 5168 170302310
PRI17 1627 180553235
PRI18 1797 181507536
PRI19 2270 188269436
PRI2 1423 173595220
PRI20 1304 185868887
PRI21 33775 121287563
PRI22 16914 162625477
PRI23 49027 118906978
PRI24 36912 126214515
PRI25 29190 42514445
PRI3 1259 181991233
PRI4 1281 177748348
PRI5 1139 173796435
PRI6 1225 179675589
PRI7 1198 176089512
PRI8 1321 167899595
PRI9 1230 177416461
ROD1 6965 178970480
ROD2 1083 195464457
ROD3 24151 153124750
ROD4 1187 194164690
ROD5 1240 192771686
ROD6 27825 136568800
ROD7 39929 51949002
STS1 90110 35004787
STS2 73486 33660824
SYN 8392 14977216
UNA 623 333867
VRL1 72814 63107499
VRL2 74052 63696098
VRL3 34705 35124442
VRT1 58484 96322736
VRT2 43496 119166366
2.2.7 Selected Per-Organism Statistics
The following table provides the number of entries and bases of DNA/RNA for
the twenty most sequenced organisms in Release 135.0 (chloroplast and mitochon-
drial sequences not included, and Whole Genome Shotgun sequences not included) :
Entries Bases Species
6574171 9743398611 Homo sapiens
4839873 5815119777 Mus musculus
702180 5565107808 Rattus norvegicus
481072 725258089 Danio rerio
350741 695203285 Drosophila melanogaster
221048 620437677 Oryza sativa (japonica cultivar-group)
730719 402816176 Zea mays
502590 394829161 Arabidopsis thaliana
567863 386355126 Brassica oleracea
13379 326808471 Macaca mulatta
427323 317823422 Gallus gallus
499207 294135749 Ciona intestinalis
390231 223252029 Bos taurus
199302 222094921 Caenorhabditis elegans
418485 207706076 Triticum aestivum
166243 191992299 Pan troglodytes
189208 170811939 Tetraodon nigroviridis
273621 166171916 Xenopus laevis
282062 156196664 Hordeum vulgare subsp. vulgare
186121 154322129 Medicago truncatula
2.2.8 Growth of GenBank
The following table lists the number of bases and the number of sequence
records in each release of GenBank, beginning with Release 3 in 1982.
From 1982 to the present, the number of bases in GenBank has doubled
approximately every 14 months.
Release Date Base Pairs Entries
3 Dec 1982 680338 606
14 Nov 1983 2274029 2427
20 May 1984 3002088 3665
24 Sep 1984 3323270 4135
25 Oct 1984 3368765 4175
26 Nov 1984 3689752 4393
32 May 1985 4211931 4954
36 Sep 1985 5204420 5700
40 Feb 1986 5925429 6642
42 May 1986 6765476 7416
44 Aug 1986 8442357 8823
46 Nov 1986 9615371 9978
48 Feb 1987 10961380 10913
50 May 1987 13048473 12534
52 Aug 1987 14855145 14020
53 Sep 1987 15514776 14584
54 Dec 1987 16752872 15465
55 Mar 1988 19156002 17047
56 Jun 1988 20795279 18226
57 Sep 1988 22019698 19044
57.1 Oct 1988 23800000 20579
58 Dec 1988 24690876 21248
59 Mar 1989 26382491 22479
60 Jun 1989 31808784 26317
61 Sep 1989 34762585 28791
62 Dec 1989 37183950 31229
63 Mar 1990 40127752 33377
64 Jun 1990 42495893 35100
65 Sep 1990 49179285 39533
66 Dec 1990 51306092 41057
67 Mar 1991 55169276 43903
68 Jun 1991 65868799 51418
69 Sep 1991 71947426 55627
70 Dec 1991 77337678 58952
71 Mar 1992 83894652 65100
72 Jun 1992 92160761 71280
73 Sep 1992 101008486 78608
74 Dec 1992 120242234 97084
75 Feb 1993 126212259 106684
76 Apr 1993 129968355 111911
77 Jun 1993 138904393 120134
78 Aug 1993 147215633 131328
79 Oct 1993 157152442 143492
80 Dec 1993 163802597 150744
81 Feb 1994 173261500 162946
82 Apr 1994 180589455 169896
83 Jun 1994 191393939 182753
84 Aug 1994 201815802 196703
85 Oct 1994 217102462 215273
86 Dec 1994 230485928 237775
87 Feb 1995 248499214 269478
88 Apr 1995 286094556 352414
89 Jun 1995 318624568 425211
90 Aug 1995 353713490 492483
91 Oct 1995 384939485 555694
92 Dec 1995 425860958 620765
93 Feb 1996 463758833 685693
94 Apr 1996 499127741 744295
95 Jun 1996 551750920 835487
96 Aug 1996 602072354 920588
97 Oct 1996 651972984 1021211
98 Dec 1996 730552938 1114581
99 Feb 1997 786898138 1192505
100 Apr 1997 842864309 1274747
101 Jun 1997 966993087 1491069
102 Aug 1997 1053474516 1610848
103 Oct 1997 1160300687 1765847
104 Dec 1997 1258290513 1891953
105 Feb 1998 1372368913 2042325
106 Apr 1998 1502542306 2209232
107 Jun 1998 1622041465 2355928
108 Aug 1998 1797137713 2532359
109 Oct 1998 2008761784 2837897
110 Dec 1998 2162067871 3043729
111 Apr 1999 2569578208 3525418
112 Jun 1999 2974791993 4028171
113 Aug 1999 3400237391 4610118
114 Oct 1999 3841163011 4864570
115 Dec 1999 4653932745 5354511
116 Feb 2000 5805414935 5691170
117 Apr 2000 7376080723 6215002
118 Jun 2000 8604221980 7077491
119 Aug 2000 9545724824 8214339
120 Oct 2000 10335692655 9102634
121 Dec 2000 11101066288 10106023
122 Feb 2001 11720120326 10896781
123 Apr 2001 12418544023 11545572
124 Jun 2001 12973707065 12243766
125 Aug 2001 13543364296 12813516
126 Oct 2001 14396883064 13602262
127 Dec 2001 15849921438 14976310
128 Feb 2002 17089143893 15465325
129 Apr 2002 19072679701 16769983
130 Jun 2002 20648748345 17471130
131 Aug 2002 22616937182 18197119
132 Oct 2002 26525934656 19808101
133 Dec 2002 28507990166 22318883
134 Feb 2003 29358082791 23035823
135 Apr 2003 31099264455 24027936
3. FILE FORMATS
The flat file examples included in this section, while not always from the
current release, are usually fairly recent. Any differences compared to the
actual records are the result of updates to the entries involved.
3.1 File Header Information
With the exception of the index files and lists of accession numbers,
each of the 481 files of a GenBank release begins with the same header,
except for the first line, which contains the file name, and the sixth line,
which contains the title of the file. The first line of the file contains
the file name in character positions 1 to 9 and the full database name
(Genetic Sequence Data Bank) starting in column 22. The brief names of
the files in this release are listed in section 2.2.
The second line contains the date of the current release in the form
`day month year', beginning in position 27. The fourth line contains
the current GenBank release number. The release number appears in
positions 48 to 52 and consists of three numbers separated by a decimal
point. The number to the left of the decimal is the major release
number. The digit to the right of the decimal indicates the version of
the major release; it is zero for the first version. The sixth line
contains a title for the file. The eighth line lists the number of
entries (loci), number of bases (or base pairs), and number of reports
of sequences (equal to number of entries in this case). These numbers are
right-justified at fixed positions. The number of entries appears in
positions 1 to 8, the number of bases in positions 16 to 26, and the
number of reports in positions 40 to 47. The third, fifth, seventh, and
ninth lines are blank.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBBCT1.SEQ Genetic Sequence Data Bank
15 April 2003
NCBI-GenBank Flat File Release 135.0
Bacterial Sequences (Part 1)
37811 loci, 97585608 bases, from 37811 reported sequences
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 1. Sample File Header
3.2 Directory Files
3.2.1 Short Directory File
The short directory file contains brief descriptions of all of the
sequence entries contained in this release. These descriptions are in
fifteen groups, one group for each of the fifteen sequence entry
data files. The first record at the beginning of a group of entries
contains the name of the group in uppercase characters, beginning in
position 21. The organism groups are PRIMATE, RODENT, OTHER MAMMAL,
OTHER VERTEBRATE, INVERTEBRATE, PLANT, BACTERIAL, STRUCTURAL RNA, VIRAL,
PHAGE, SYNTHETIC, UNANNOTATED, EXPRESSED SEQUENCE TAG, PATENT, or
SEQUENCE TAGGED SITE. The second record is blank.
Each record in the short directory contains the sequence entry name
(LOCUS) in the first 12 positions, followed by a brief definition of
the sequence beginning in column 13. The definition is truncated (at
the end of a word) to leave room at the right margin for at least one
space, the sequence length, and the letters `bp'. The length of the
sequence is printed right-justified to column 77, followed by the
letters `bp' in columns 78 and 79. The next-to-last record for a group
has `ZZZZZZZZZZ' in its first ten positions (where the entry name
would normally appear). The last record is a blank line. An example of
the short directory file format, showing the descriptions of the last
entries in the Other Vertebrate sequence data file and the first
entries of the Invertebrate sequence data file, is reproduced below:
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
ZEFWNT1G3 B.rerio wnt-1 gene (exon 3) for wnt-1 protein. 266bp
ZEFWNT1G4 B.rerio wnt-1 gene (exon 4) for wnt-1 protein. 647bp
ZEFZF54 Zebrafish homeotic gene ZF-54. 246bp
ZEFZFEN Zebrafish engrailed-like homeobox sequence. 327bp
ZZZZZZZZZZ
INVERTEBRATE
AAHAV33A Acanthocheilonema viteae pepsin-inhibitor-like-protein 1048bp
ACAAC01 Acanthamoeba castelani gene encoding actin I. 1571bp
ACAACTPH Acanthamoeba castellanii actophorin mRNA, complete cds. 671bp
ACAMHCA A.castellanii non-muscle myosin heavy chain gene, partial 5894bp
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 2. Short Directory File
3.3 Index Files
There are six files containing indices to the entries in this release:
Accession number index file (Accession and Version)
Secondary accession number index file
Keyword phrase index file
Author name index file
Journal citation index file
Gene name index file
The index keys (accession numbers, keywords, authors, journals, and
gene symbols.) of an index are sorted alphabetically. All index keys
appear in uppercase characters even though they appear in mixed case
in the sequence entries. Following each index key, the identifiers of the
sequence entries containing that key are listed (LOCUS name,
division abbreviation, and primary accession number). The division
abbreviations are:
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags)
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites)
15. GSS - GSS sequences (genome survey sequences)
16. HTG - HTGS sequences (high throughput genomic sequences)
17. HTC - HTC sequences (high throughput cDNA sequences)
A line-oriented, TAB-delimited format is utilized for the gbaut.idx,
gbgen.idx, gbjou.idx, gbkey.idx, and gbsec.idx indexes. Each index
key is presented on its own line, and is followed by a
LOCUS/Division/Accession triplet for every record containing the key:
Indexed-Term
LOCUS-name1 Div-code1 Accession1
LOCUS-name2 Div-code2 Accession2
LOCUS-name3 Div-code3 Accession3
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
(H+,K+)-ATPASE BETA-SUBUNIT$
^IRATHKATPB^IROD^IM55655$
^IMUSATP4B1^IROD^IM64685$
^IMUSATP4B2^IROD^IM64686$
^IMUSATP4B3^IROD^IM64687$
^IMUSATP4B4^IROD^IM64688$
^IDOGATPASEB^IMAM^IM76486$
When viewed by a file browser such as 'less' or 'more' :
(H+,K+)-ATPASE BETA-SUBUNIT
RATHKATPB ROD M55655
MUSATP4B1 ROD M64685
MUSATP4B2 ROD M64686
MUSATP4B3 ROD M64687
MUSATP4B4 ROD M64688
DOGATPASEB MAM M76486
Note that the index keys can be distinguished from LOCUS/DIV/ACCESSION
by the fact that they do not start with a TAB character. So one can
extract just the terms via simple text-processing:
perl -ne 'print unless /^\s+/' < gbkey.idx > terms.gbkey
The format of the primary accession number index file is slightly
different, with each indexed key (Accession.Version) present on
the same line as the LOCUS/Division/Accession triplet:
Accession1.Version1 Locus-name1 Div-code1 Accession1
Accession2.Version2 Locus-name2 Div-code2 Accession2
....
Here is an example of the format, in which TAB characters are displayed
as ^I, and carriage-returns/newlines as $ :
AC000102.1^IAC000102^IPRI^IAC000102$
AC000103.1^IAC000103^IPLN^IAC000103$
AC000104.1^IF19P19^IPLN^IAC000104$
AC000105.40^IAC000105^IPRI^IAC000105$
AC000106.1^IF7G19^IPLN^IAC000106$
AC000107.1^IAC000107^IPLN^IAC000107$
AC000108.1^IAC000108^IBCT^IAC000108$
AC000109.1^IHSAC000109^IPRI^IAC000109$
AC000110.1^IHSAC000110^IPRI^IAC000110$
When viewed by a file browser such as 'less' or 'more' :
AC000102.1 AC000102 PRI AC000102
AC000103.1 AC000103 PLN AC000103
AC000104.1 F19P19 PLN AC000104
AC000105.40 AC000105 PRI AC000105
AC000106.1 F7G19 PLN AC000106
AC000107.1 AC000107 PLN AC000107
AC000108.1 AC000108 BCT AC000108
AC000109.1 HSAC000109 PRI AC000109
AC000110.1 HSAC000110 PRI AC000110
3.3.1 Accession Number Index File - gbacc.idx
Accession numbers are unique six character or eight-character alphanumeric
identifiers of GenBank database entries. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. Accessions provide an unchanging identifier
for the data with which they are associated, and we encourage you to cite
accession numbers whenever you refer to data from GenBank.
GenBank entries can have both 'primary' and 'secondary' accessions
associated with them (see Section 3.5.6). Only primary accessions are present
in the gbacc.idx index.
3.3.2 Keyword Phrase Index File - gbkey.idx
Keyword phrases consist of names for gene products and other
characteristics of sequence entries.
3.3.3 Author Name Index File - gbaut*.idx
The author name index files list all of the author names that appear
in the references within sequence records.
3.3.4 Journal Citation Index File - gbjou.idx
The journal citation index file lists all of the citations that appear
in the references within sequence records.. All citations are truncated
to 80 characters.
3.3.5 Gene Name Index - gbgen.idx
The /gene qualifiers of many GenBank entries contain values other than
official gene symbols, such as the product or the standard name of the gene.
Hence, NCBI has chosen to build an index (gbgen.idx) more like a keyword index
for this field, using both the GenBank /gene qualifier and the 'Gene.locus'
fields from the NCBI internal database as keys.
3.4 Sequence Entry Files
GenBank releases contain one or more sequence entry data files, one
for each "division" of GenBank.
3.4.1 File Organization
Each of these files has the same format and consists of two parts:
header information (described in section 3.1) and sequence entries for
that division (described in the following sections).
3.4.2 Entry Organization
In the second portion of a sequence entry file (containing the
sequence entries for that division), each record (line) consists of
two parts. The first part is found in positions 1 to 10 and may
contain:
1. A keyword, beginning in column 1 of the record (e.g., REFERENCE is
a keyword).
2. A subkeyword beginning in column 3, with columns 1 and 2 blank
(e.g., AUTHORS is a subkeyword of REFERENCE). Or a subkeyword beginning
in column 4, with columns 1, 2, and 3 blank (e.g., PUBMED is a
subkeyword of REFERENCE).
3. Blank characters, indicating that this record is a continuation of
the information under the keyword or subkeyword above it.
4. A code, beginning in column 6, indicating the nature of an entry
(feature key) in the FEATURES table; these codes are described in
Section 3.4.12.1 below.
5. A number, ending in column 9 of the record. This number occurs in
the portion of the entry describing the actual nucleotide sequence and
designates the numbering of sequence positions.
6. Two slashes (//) in positions 1 and 2, marking the end of an entry.
The second part of each sequence entry record contains the information
appropriate to its keyword, in positions 13 to 80 for keywords and
positions 11 to 80 for the sequence.
The following is a brief description of each entry field. Detailed
information about each field may be found in Sections 3.4.4 to 3.4.14.
LOCUS - A short mnemonic name for the entry, chosen to suggest the
sequence's definition. Mandatory keyword/exactly one record.
DEFINITION - A concise description of the sequence. Mandatory
keyword/one or more records.
ACCESSION - The primary accession number is a unique, unchanging
code assigned to each entry. (Please use this code when citing
information from GenBank.) Mandatory keyword/one or more records.
VERSION - A compound identifier consisting of the primary
accession number and a numeric version number associated with the
current version of the sequence data in the record. This is followed
by an integer key (a "GI") assigned to the sequence by NCBI.
Mandatory keyword/exactly one record.
NID - An alternative method of presenting the NCBI GI
identifier (described above). The NID is obsolete and was removed
from the GenBank flatfile format in December 1999.
KEYWORDS - Short phrases describing gene products and other
information about an entry. Mandatory keyword in all annotated
entries/one or more records.
SEGMENT - Information on the order in which this entry appears in a
series of discontinuous sequences from the same molecule. Optional
keyword (only in segmented entries)/exactly one record.
SOURCE - Common name of the organism or the name most frequently used
in the literature. Mandatory keyword in all annotated entries/one or
more records/includes one subkeyword.
ORGANISM - Formal scientific name of the organism (first line)
and taxonomic classification levels (second and subsequent lines).
Mandatory subkeyword in all annotated entries/two or more records.
REFERENCE - Citations for all articles containing data reported
in this entry. Includes seven subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Optional
subkeyword/one or more records.
CONSRTM - Lists the collective names of consortiums associated
with the citation (eg, International Human Genome Sequencing Consortium),
rather than individual author names. Optional subkeyword/one or more records.
TITLE - Full title of citation. Optional subkeyword (present
in all but unpublished citations)/one or more records.
JOURNAL - Lists the journal name, volume, year, and page
numbers of the citation. Mandatory subkeyword/one or more records.
MEDLINE - Provides the Medline unique identifier for a
citation. Optional subkeyword/one record.
PUBMED - Provides the PubMed unique identifier for a
citation. Optional subkeyword/one record.
REMARK - Specifies the relevance of a citation to an
entry. Optional subkeyword/one or more records.
COMMENT - Cross-references to other sequence entries, comparisons to
other collections, notes of changes in LOCUS names, and other remarks.
Optional keyword/one or more records/may include blank records.
FEATURES - Table containing information on portions of the
sequence that code for proteins and RNA molecules and information on
experimentally determined sites of biological significance. Optional
keyword/one or more records.
BASE COUNT - Summary of the number of occurrences of each base
code in the sequence. Mandatory keyword/exactly one record.
ORIGIN - Specification of how the first base of the reported sequence
is operationally located within the genome. Where possible, this
includes its location within a larger genetic map. Mandatory
keyword/exactly one record.
- The ORIGIN line is followed by sequence data (multiple records).
// - Entry termination symbol. Mandatory at the end of an
entry/exactly one record.
3.4.3 Sample Sequence Data File
An example of a complete sequence entry file follows. (This example
has only two entries.) Note that in this example, as throughout the
data bank, numbers in square brackets indicate items in the REFERENCE
list. For example, in ACARR58S, [1] refers to the paper by Mackay, et
al.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
GBSMP.SEQ Genetic Sequence Data Bank
15 December 1992
GenBank Flat File Release 74.0
Structural RNA Sequences
2 loci, 236 bases, from 2 reported sequences
LOCUS AAURRA 118 bp ss-rRNA RNA 16-JUN-1986
DEFINITION A.auricula-judae (mushroom) 5S ribosomal RNA.
ACCESSION K03160
VERSION K03160.1 GI:173593
KEYWORDS 5S ribosomal RNA; ribosomal RNA.
SOURCE A.auricula-judae (mushroom) ribosomal RNA.
ORGANISM Auricularia auricula-judae
Eukaryota; Fungi; Eumycota; Basidiomycotina; Phragmobasidiomycetes;
Heterobasidiomycetidae; Auriculariales; Auriculariaceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Huysmans,E., Dams,E., Vandenberghe,A. and De Wachter,R.
TITLE The nucleotide sequences of the 5S rRNAs of four mushrooms and
their use in studying the phylogenetic position of basidiomycetes
among the eukaryotes
JOURNAL Nucleic Acids Res. 11, 2871-2880 (1983)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 34 c 34 g 23 t
ORIGIN 5' end of mature rRNA.
1 atccacggcc ataggactct gaaagcactg catcccgtcc gatctgcaaa gttaaccaga
61 gtaccgccca gttagtacca cggtggggga ccacgcggga atcctgggtg ctgtggtt
//
LOCUS ABCRRAA 118 bp ss-rRNA RNA 15-SEP-1990
DEFINITION Acetobacter sp. (strain MB 58) 5S ribosomal RNA, complete sequence.
ACCESSION M34766
VERSION M34766.1 GI:173603
KEYWORDS 5S ribosomal RNA.
SOURCE Acetobacter sp. (strain MB 58) rRNA.
ORGANISM Acetobacter sp.
Prokaryotae; Gracilicutes; Scotobacteria; Aerobic rods and cocci;
Azotobacteraceae.
REFERENCE 1 (bases 1 to 118)
AUTHORS Bulygina,E.S., Galchenko,V.F., Govorukhina,N.I., Netrusov,A.I.,
Nikitin,D.I., Trotsenko,Y.A. and Chumakov,K.M.
TITLE Taxonomic studies of methylotrophic bacteria by 5S ribosomal RNA
sequencing
JOURNAL J. Gen. Microbiol. 136, 441-446 (1990)
FEATURES Location/Qualifiers
rRNA 1..118
/note="5S ribosomal RNA"
BASE COUNT 27 a 40 c 32 g 17 t 2 others
ORIGIN
1 gatctggtgg ccatggcggg agcaaatcag ccgatcccat cccgaactcg gccgtcaaat
61 gccccagcgc ccatgatact ctgcctcaag gcacggaaaa gtcggtcgcc gccagayy
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 9. Sample Sequence Data File
3.4.4 LOCUS Format
The items of information contained in the LOCUS record are always
found in fixed positions. The locus name (or entry name), which is
always sixteen characters or less, begins in position 13. The locus name
is designed to help group entries with similar sequences: the first
three characters usually designate the organism; the fourth and fifth
characters can be used to show other group designations, such as gene
product; for segmented entries the last character is one of a series
of sequential integers.
The number of bases or base pairs in the sequence ends in position 40.
The letters `bp' are in positions 42 to 43. Positions 45 to 47 provide
the number of strands of the sequence. Positions 48 to 53 indicate the
type of molecule sequenced. Topology of the molecule is indicated in
positions 56 to 63.
GenBank sequence entries are divided among many different
'divisions'. Each entry's division is specified by a three-letter code
in positions 65 to 67. See Section 3.3 for an explanation of division
codes.
Positions 69 to 79 of the record contain the date the entry was
entered or underwent any substantial revisions, such as the addition
of newly published data, in the form dd-MMM-yyyy.
The detailed format for the LOCUS line format is as follows:
Positions Contents
--------- --------
01-05 'LOCUS'
06-12 spaces
13-28 Locus name
29-29 space
30-40 Length of sequence, right-justified
41-41 space
42-43 bp
44-44 space
45-47 spaces, ss- (single-stranded), ds- (double-stranded), or
ms- (mixed-stranded)
48-53 NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),
mRNA (messenger RNA), uRNA (small nuclear RNA), snRNA,
snoRNA. Left justified.
54-55 space
56-63 'linear' followed by two spaces, or 'circular'
64-64 space
65-67 The division code (see Section 3.3)
68-68 space
69-79 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
Although each of these data values can be found at column-specific
positions, we encourage those who parse the contents of the LOCUS
line to use a token-based approach. This will prevent the need for
software changes if the spacing of the data values ever has to be
modified.
3.4.5 DEFINITION Format
The DEFINITION record gives a brief description of the sequence,
proceeding from general to specific. It starts with the common name of
the source organism, then gives the criteria by which this sequence is
distinguished from the remainder of the source genome, such as the
gene name and what it codes for, or the protein name and mRNA, or some
description of the sequence's function (if the sequence is
non-coding). If the sequence has a coding region, the description may
be followed by a completeness qualifier, such as cds (complete coding
sequence). There is no limit on the number of lines that may be part
of the DEFINITION. The last line must end with a period.
3.4.5.1 DEFINITION Format for NLM Entries
The DEFINITION line for entries derived from journal-scanning at the NLM is
an automatically generated descriptive summary that accompanies each DNA and
protein sequence. It contains information derived from fields in a database
that summarize the most important attributes of the sequence. The DEFINITION
lines are designed to supplement the accession number and the sequence itself
as a means of uniquely and completely specifying DNA and protein sequences. The
following are examples of NLM DEFINITION lines:
NADP-specific isocitrate dehydrogenase [swine, mRNA, 1 gene, 1585 nt]
94 kda fiber cell beaded-filament structural protein [rats, lens, mRNA
Partial, 1 gene, 1873 nt]
inhibin alpha {promoter and exons} [mice, Genomic, 1 gene, 1102 nt, segment
1 of 2]
cefEF, cefG=acetyl coenzyme A:deacetylcephalosporin C o-acetyltransferase
[Acremonium chrysogenum, Genomic, 2 genes, 2639 nt]
myogenic factor 3, qmf3=helix-loop-helix protein [Japanese quails,
embryo, Peptide Partial, 246 aa]
The first part of the definition line contains information describing
the genes and proteins represented by the molecular sequences. This can
be gene locus names, protein names and descriptions that replace or augment
actual names. Gene and gene product are linked by "=". Any special
identifying terms are presented within brackets, such as: {promoter},
{N-terminal}, {EC 2.13.2.4}, {alternatively spliced}, or {3' region}.
The second part of the definition line is delimited by square brackets, '[]',
and provides details about the molecule type and length. The biological
source, i.e., genus and species or common name as cited by the author.
Developmental stage, tissue type and strain are included if available.
The molecule types include: Genomic, mRNA, Peptide. and Other Genomic
Material. Genomic molecules are assumed to be partial sequence unless
"Complete" is specified, whereas mRNA and peptide molecules are assumed
to be complete unless "Partial" is noted.
3.4.6 ACCESSION Format
This field contains a series of six-character and/or eight-character
identifiers called 'accession numbers'. The six-character accession
number format consists of a single uppercase letter, followed by 5 digits.
The eight-character accession number format consists of two uppercase
letters, followed by 6 digits. The 'primary', or first, of the accession
numbers occupies positions 13 to 18 (6-character format) or positions
13 to 20 (8-character format). Subsequent 'secondary' accession numbers
(if present) are separated from the primary, and from each other, by a
single space. In some cases, multiple lines of secondary accession
numbers might be present, starting at position 13.
The primary accession number of a GenBank entry provides a stable identifier
for the biological object that the entry represents. Accessions do not change
when the underlying sequence data or associated features change.
Secondary accession numbers arise for a number of reasons. For example, a
single accession number may initially be assigned to a sequence described in
a publication. If it is later discovered that the sequence must be entered
into the database as multiple entries, each entry would receive a new primary
accession number, and the original accession number would appear as a secondary
accession number on each of the new entries.
3.4.7 VERSION Format
This line contains two types of identifiers for a GenBank database entry:
a compound accession number and an NCBI GI identifier.
LOCUS AF181452 1294 bp DNA PLN 12-OCT-1999
DEFINITION Hordeum vulgare dehydrin (Dhn2) gene, complete cds.
ACCESSION AF181452
VERSION AF181452.1 GI:6017929
^^^^^^^^^^ ^^^^^^^^^^
Compound NCBI GI
Accession Identifier
Number
A compound accession number consists of two parts: a stable, unchanging
primary-accession number portion (see Section 3.4.6 for a description of
accession numbers), and a sequentially increasing numeric version number.
The accession and version numbers are separated by a period. The initial
version number assigned to a new sequence is one. Compound accessions are
often referred to as "Accession.Version" .
An accession number allows one to retrieve the same biological object in the
database, regardless of any changes that are made to the entry over time. But
those changes can include changes to the sequence data itself, which is of
fundamental importance to many database users. So a numeric version number is
associated with the sequence data in every database entry. If an entry (for
example, AF181452) undergoes two sequence changes, its compound accession
number on the VERSION line would start as AF181452.1 . After the first sequence
change this would become: AF181452.2 . And after the second change: AF181452.3 .
The NCBI GI identifier of the VERSION line also serves as a method for
identifying the sequence data that has existed for a database entry over
time. GI identifiers are numeric values of one or more digits. Since they
are integer keys, they are less human-friendly than the Accession.Version
system described above. Returning to our example for AF181452, it was
initially assigned GI 6017929. If the sequence changes, a new integer GI will
be assigned, perhaps 7345003 . And after the second sequence change, perhaps
the GI would become 10456892 .
Why are both these methods for identifying the version of the sequence
associated with a database entry in use? For two reasons:
- Some data sources processed by NCBI for incorporation into its Entrez
sequence retrieval system do not version their own sequences.
- GIs provide a uniform, integer identifier system for every sequence
NCBI has processed. Some products and systems derived from (or reliant
upon) NCBI products and services prefer to use these integer identifiers
because they can all be processed in the same manner.
GenBank Releases contain only the most recent versions of all sequences
in the database. However, older versions can be obtained via GI-based or
Accession.Version-based queries with NCBI's web-Entrez and network-Entrez
applications. A sequence revision history web page is also available:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/girevhist
NOTE: All the version numbers for the compound Accession.Version identifier
system were initialized to a value of one in February 1999, when that
system was introduced.
3.4.8 KEYWORDS Format
The KEYWORDS field does not appear in unannotated entries, but is
required in all annotated entries. Keywords are separated by
semicolons; a "keyword" may be a single word or a phrase consisting of
several words. Each line in the keywords field ends in a semicolon;
the last line ends with a period. If no keywords are included in the
entry, the KEYWORDS record contains only a period.
3.4.9 SEGMENT Format
The SEGMENT keyword is used when two (or more) entries of known
relative orientation are separated by a short (<10 kb) stretch of DNA.
It is limited to one line of the form `n of m', where `n' is the
segment number of the current entry and `m' is the total number of
segments.
3.4.10 SOURCE Format
The SOURCE field consists of two parts. The first part is found after
the SOURCE keyword and contains free-format information including an
abbreviated form of the organism name followed by a molecule type;
multiple lines are allowed, but the last line must end with a period.
The second part consists of information found after the ORGANISM
subkeyword. The formal scientific name for the source organism (genus
and species, where appropriate) is found on the same line as ORGANISM.
The records following the ORGANISM line list the taxonomic
classification levels, separated by semicolons and ending with a
period.
3.4.11 REFERENCE Format
The REFERENCE field consists of five parts: the keyword REFERENCE, and
the subkeywords AUTHORS, TITLE (optional), JOURNAL, MEDLINE (optional),
PUBMED (optional), and REMARK (optional).
The REFERENCE line contains the number of the particular reference and
(in parentheses) the range of bases in the sequence entry reported in
this citation. Additional prose notes may also be found within the
parentheses. The numbering of the references does not reflect
publication dates or priorities.
The AUTHORS line lists the authors in the order in which they appear
in the cited article. Last names are separated from initials by a
comma (no space); there is no comma before the final `and'. The list
of authors ends with a period. The TITLE line is an optional field,
although it appears in the majority of entries. It does not appear in
unpublished sequence data entries that have been deposited directly
into the GenBank data bank, the EMBL Nucleotide Sequence Data Library,
or the DNA Data Bank of Japan. The TITLE field does not end with a
period.
The JOURNAL line gives the appropriate literature citation for the
sequence in the entry. The word `Unpublished' will appear after the
JOURNAL subkeyword if the data did not appear in the scientific
literature, but was directly deposited into the data bank. For
published sequences the JOURNAL line gives the Thesis, Journal, or
Book citation, including the year of publication, the specific
citation, or In press.
The MEDLINE line provides the National Library of Medicine's Medline
unique identifier for a citation (if known). Medline UIs are 8 digit
numbers.
The PUBMED line provides the PubMed unique identifier for a citation
(if known). PUBMED ids are numeric, and are record identifiers for article
abstracts in the PubMed database :
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Citations in PubMed that do not fall within Medline's scope will have only
a PUBMED identifier. Similarly, citations that *are* in Medline's scope but
which have not yet been assigned Medline UIs will have only a PUBMED identifier.
If a citation is present in both the PubMed and Medline databases, both a
MEDLINE and a PUBMED line will be present.
The REMARK line is a textual comment that specifies the relevance
of the citation to the entry.
3.4.12 FEATURES Format
GenBank releases use a feature table format designed jointly by
GenBank, the EMBL Nucleotide Sequence Data Library, and the DNA Data
Bank of Japan. This format is in use by all three databases. The
most complete and accurate Feature Table documentation can be found
on the Web at:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
Any discrepancy between the abbreviated feature table description
of these release notes and the complete documentation on the Web
should be resolved in favor of the version at the above URL.
The Feature Table specification is also available as a printed
document: `The DDBJ/EMBL/GenBank Feature Table: Definition'. Contact
GenBank at the address shown on the first page of these Release Notes
if you would like a copy.
The feature table contains information about genes and gene products,
as well as regions of biological significance reported in the
sequence. The feature table contains information on regions of the
sequence that code for proteins and RNA molecules. It also enumerates
differences between different reports of the same sequence, and
provides cross-references to other data collections, as described in
more detail below.
The first line of the feature table is a header that includes the
keyword `FEATURES' and the column header `Location/Qualifier.' Each
feature consists of a descriptor line containing a feature key and a
location (see sections below for details). If the location does not
fit on this line, a continuation line may follow. If further
information about the feature is required, one or more lines
containing feature qualifiers may follow the descriptor line.
The feature key begins in column 6 and may be no more than 15
characters in length. The location begins in column 22. Feature
qualifiers begin on subsequent lines at column 22. Location,
qualifier, and continuation lines may extend from column 22 to 80.
Feature tables are required, due to the mandatory presence of the
source feature. The sections below provide a brief introduction to
the feature table format.
3.4.12.1 Feature Key Names
The first column of the feature descriptor line contains the feature
key. It starts at column 6 and can continue to column 20. The list of
valid feature keys is shown below.
Remember, the most definitive documentation for the feature table can
be found at:
http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
allele Obsolete; see variation feature key
attenuator Sequence related to transcription termination
C_region Span of the C immunological feature
CAAT_signal `CAAT box' in eukaryotic promoters
CDS Sequence coding for amino acids in protein (includes
stop codon)
conflict Independent sequence determinations differ
D-loop Displacement loop
D_segment Span of the D immunological feature
enhancer Cis-acting enhancer of promoter function
exon Region that codes for part of spliced mRNA
gene Region that defines a functional gene, possibly
including upstream (promotor, enhancer, etc)
and downstream control elements, and for which
a name has been assigned.
GC_signal `GC box' in eukaryotic promoters
iDNA Intervening DNA eliminated by recombination
intron Transcribed region excised by mRNA splicing
J_region Span of the J immunological feature
LTR Long terminal repeat
mat_peptide Mature peptide coding region (does not include stop codon)
misc_binding Miscellaneous binding site
misc_difference Miscellaneous difference feature
misc_feature Region of biological significance that cannot be described
by any other feature
misc_recomb Miscellaneous recombination feature
misc_RNA Miscellaneous transcript feature not defined by other RNA keys
misc_signal Miscellaneous signal
misc_structure Miscellaneous DNA or RNA structure
modified_base The indicated base is a modified nucleotide
mRNA Messenger RNA
mutation Obsolete: see variation feature key
N_region Span of the N immunological feature
old_sequence Presented sequence revises a previous version
polyA_signal Signal for cleavage & polyadenylation
polyA_site Site at which polyadenine is added to mRNA
precursor_RNA Any RNA species that is not yet the mature RNA product
prim_transcript Primary (unprocessed) transcript
primer Primer binding region used with PCR
primer_bind Non-covalent primer binding site
promoter A region involved in transcription initiation
protein_bind Non-covalent protein binding site on DNA or RNA
RBS Ribosome binding site
rep_origin Replication origin for duplex DNA
repeat_region Sequence containing repeated subsequences
repeat_unit One repeated unit of a repeat_region
rRNA Ribosomal RNA
S_region Span of the S immunological feature
satellite Satellite repeated sequence
scRNA Small cytoplasmic RNA
sig_peptide Signal peptide coding region
snRNA Small nuclear RNA
source Biological source of the sequence data represented by
a GenBank record. Mandatory feature, one or more per record.
For organisms that have been incorporated within the
NCBI taxonomy database, an associated /db_xref="taxon:NNNN"
qualifier will be present (where NNNNN is the numeric
identifier assigned to the organism within the NCBI taxonomy
database).
stem_loop Hair-pin loop structure in DNA or RNA
STS Sequence Tagged Site; operationally unique sequence that
identifies the combination of primer spans used in a PCR assay
TATA_signal `TATA box' in eukaryotic promoters
terminator Sequence causing transcription termination
transit_peptide Transit peptide coding region
transposon Transposable element (TN)
tRNA Transfer RNA
unsure Authors are unsure about the sequence in this region
V_region Span of the V immunological feature
variation A related population contains stable mutation
- (hyphen) Placeholder
-10_signal `Pribnow box' in prokaryotic promoters
-35_signal `-35 box' in prokaryotic promoters
3'clip 3'-most region of a precursor transcript removed in processing
3'UTR 3' untranslated region (trailer)
5'clip 5'-most region of a precursor transcript removed in processing
5'UTR 5' untranslated region (leader)
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
1. A single base;
2. A contiguous span of bases;
3. A site between two bases;
4. A single base chosen from a range of bases;
5. A single base chosen from among two or more specified bases;
6. A joining of sequence spans;
7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).
A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
of the range is beyond the specified base number.
A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.
Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.
complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.
join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.
order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.
3.4.12.3 Feature Qualifiers
Qualifiers provide additional information about features. They take
the form of a slash (/) followed by a qualifier name and, if
applicable, an equal sign (=) and a qualifier value. Feature
qualifiers begin at column 22.
Qualifiers convey many types of information. Their values can,
therefore, take several forms:
1. Free text;
2. Controlled vocabulary or enumerated values;
3. Citations or reference numbers;
4. Sequences;
5. Feature labels.
Text qualifier values must be enclosed in double quotation marks. The
text can consist of any printable characters (ASCII values 32-126
decimal). If the text string includes double quotation marks, each set
must be `escaped' by placing a double quotation mark in front of it
(e.g., /note="This is an example of ""escaped"" quotation marks").
Some qualifiers require values selected from a limited set of choices.
For example, the `/direction' qualifier has only three values `left,'
`right,' or `both.' These are called controlled vocabulary qualifier
values. Controlled qualifier values are not case sensitive; they can
be entered in any combination of upper- and lowercase without changing
their meaning.
Citation or published reference numbers for the entry should be
enclosed in square brackets ([]) to distinguish them from other
numbers.
A literal sequence of bases (e.g., "atgcatt") should be enclosed in
quotation marks. Literal sequences are distinguished from free text by
context. Qualifiers that take free text as their values do not take
literal sequences, and vice versa.
The `/label=' qualifier takes a feature label as its qualifier.
Although feature labels are optional, they allow unambiguous
references to the feature. The feature label identifies a feature
within an entry; when combined with the accession number and the name
of the data bank from which it came, it is a unique tag for that
feature. Feature labels must be unique within an entry, but can be the
same as a feature label in another entry. Feature labels are not case
sensitive; they can be entered in any combination of upper-and
lowercase without changing their meaning.
The following is a partial list of feature qualifiers.
/anticodon Location of the anticodon of tRNA and the amino acid
for which it codes
/bound_moiety Moiety bound
/citation Reference to a citation providing the claim of or
evidence for a feature
/codon Specifies a codon that is different from any found in the
reference genetic code
/codon_start Indicates the first base of the first complete codon
in a CDS (as 1 or 2 or 3)
/cons_splice Identifies intron splice sites that do not conform to
the 5'-GT... AG-3' splice site consensus
/db_xref A database cross-reference; pointer to related information
in another database. A description of all cross-references
can be found at:
http://www.ncbi.nlm.nih.gov/collab/db_xref.html
/direction Direction of DNA replication
/EC_number Enzyme Commission number for the enzyme product of the
sequence
/evidence Value indicating the nature of supporting evidence
/frequency Frequency of the occurrence of a feature
/function Function attributed to a sequence
/gene Symbol of the gene corresponding to a sequence region (usable
with all features)
/label A label used to permanently identify a feature
/map Map position of the feature in free-format text
/mod_base Abbreviation for a modified nucleotide base
/note Any comment or additional information
/number A number indicating the order of genetic elements
(e.g., exons or introns) in the 5 to 3 direction
/organism Name of the organism that is the source of the
sequence data in the record.
/partial Differentiates between complete regions and partial ones
/phenotype Phenotype conferred by the feature
/product Name of a product encoded by a coding region (CDS)
feature
/pseudo Indicates that this feature is a non-functional
version of the element named by the feature key
/rpt_family Type of repeated sequence; Alu or Kpn, for example
/rpt_type Organization of repeated sequence
/rpt_unit Identity of repeat unit that constitutes a repeat_region
/standard_name Accepted standard name for this feature
/transl_except Translational exception: single codon, the translation
of which does not conform to the reference genetic code
/translation Amino acid translation of a coding region
/type Name of a strain if different from that in the SOURCE field
/usedin Indicates that feature is used in a compound feature
in another entry
3.4.12.4 Cross-Reference Information
One type of information in the feature table lists cross-references to
the annual compilation of transfer RNA sequences in Nucleic Acids
Research, which has kindly been sent to us on CD-ROM by Dr. Sprinzl.
Each tRNA entry of the feature table contains a /note= qualifier that
includes a reference such as `(NAR: 1234)' to identify code 1234 in
the NAR compilation. When such a cross-reference appears in an entry
that contains a gene coding for a transfer RNA molecule, it refers to
the code in the tRNA gene compilation. Similar cross-references in
entries containing mature transfer RNA sequences refer to the
companion compilation of tRNA sequences published by D.H. Gauss and M.
Sprinzl in Nucleic Acids Research.
3.4.12.5 Feature Table Examples
In the first example a number of key names, feature locations, and
qualifiers are illustrated, taken from different sequences. The first
table entry is a coding region consisting of a simple span of bases
and including a /gene qualifier. In the second table entry, an NAR
cross-reference is given (see the previous section for a discussion of
these cross-references). The third and fourth table entries use the
symbols `<`and `>' to indicate that the beginning or end of the
feature is beyond the range of the presented sequence. In the fifth
table entry, the symbol `^' indicates that the feature is between
bases.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
CDS 5..1261
/product="alpha-1-antitrypsin precursor"
/map="14q32.1"
/gene="PI"
tRNA 1..87
/note="Leu-tRNA-CAA (NAR: 1057)"
/anticodon=(pos:35..37,aa:Leu)
mRNA 1..>66
/note="alpha-1-acid glycoprotein mRNA"
transposon <1..267
/note="insertion element IS5"
misc_recomb 105^106
/note="B.subtilis DNA end/IS5 DNA start"
conflict 258
/replace="t"
/citation=[2]
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 10. Feature Table Entries
The next example shows the representation for a CDS that spans more
than one entry.
1 10 20 30 40 50 60 70 79
---------+---------+---------+---------+---------+---------+---------+---------
LOCUS HUMPGAMM1 3688 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M)
gene, 5' end.
ACCESSION M55673 M25818 M27095
KEYWORDS phosphoglycerate mutase.
SEGMENT 1 of 2
.
.
.
FEATURES Location/Qualifiers
CAAT_signal 1751..1755
/gene="PGAM-M"
TATA_signal 1791..1799
/gene="PGAM-M"
exon 1820..2274
/number=1
/EC_number="5.4.2.1"
/gene="PGAM-M"
intron 2275..2377
/number=1
/gene="PGAM2"
exon 2378..2558
/number=2
/gene="PGAM-M"
.
.
.
//
LOCUS HUMPGAMM2 677 bp ds-DNA PRI 15-OCT-1990
DEFINITION Human phosphoglycerate mutase (muscle specific isozyme) (PGAM-M),
exon 3.
ACCESSION M55674 M25818 M27096
KEYWORDS phosphoglycerate mutase.
SEGMENT 2 of 2
.
.
.
FEATURES Location/Qualifiers
exon 255..457
/number=3
/gene="PGAM-M"
intron order(M55673:2559..>3688,<1..254)
/number=2
/gene="PGAM-M"
mRNA join(M55673:1820..2274,M55673:2378..2558,255..457)
/gene="PGAM-M"
CDS join(M55673:1861..2274,M55673:2378..2558,255..421)
/note="muscle-specific isozyme"
/gene="PGAM2"
/product="phosphoglycerate mutase"
/codon_start=1
/translation="MATHRLVMVRHGESTWNQENRFCGWFDAELSEKGTEEAKRGAKA
IKDAKMEFDICYTSVLKRAIRTLWAILDGTDQMWLPVVRTWRLNERHYGGLTGLNKAE
TAAKHGEEQVKIWRRSFDIPPPPMDEKHPYYNSISKERRYAGLKPGELPTCESLKDTI
ARALPFWNEEIVPQIKAGKRVLIAAHGNSLRGIVKHLEGMSDQAIMELNLPTGIPIVY
ELNKELKPTKPMQFLGDEETVRKAMEAVAAQGKAK"
.
.
.
//
---------+---------+---------+---------+---------+---------+---------+---------
1 10 20 30 40 50 60 70 79
Example 11. Joining Sequences
3.4.13 ORIGIN Format
The ORIGIN record may be left blank, may appear as `Unreported.' or
may give a local pointer to the sequence start, usually involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). The ORIGIN record ends in a period if it
contains data, but does not include the period if the record is left
empty (in contrast to the KEYWORDS field which contains a period
rather than being left blank).
3.4.14 SEQUENCE Format
The nucleotide sequence for an entry is found in the records following
the ORIGIN record. The sequence is reported in the 5 to 3 direction.
There are sixty bases per record, listed in groups of ten bases
followed by a blank, starting at position 11 of each record. The
number of the first nucleotide in the record is given in columns 4 to
9 (right justified) of the record.
4. ALTERNATE RELEASES
NCBI is supplying sequence data in the GenBank flat file format to
maintain compatibility with existing software which require that
particular format. Although we have made every effort to ensure
that these data are presented in the traditional flat file format,
if you encounter any problems in using these data with software which
is based upon the flat file format, please contact us at:
[email protected]
The flat file is just one of many possible report formats that can be
generated from the richer representation supported by the ASN.1 form of the
data. Developers of new software tools should consider using the ASN.1 form
directly to take advantage of those features. Documentation and a Software
Developer's Toolkit for ASN.1 are available through NCBI. You may call NCBI
at (301)496-2475, or subscribe to a developers' electronic newsgroup by
sending your name, address, affiliation, and e-mail address to:
[email protected]
The Software Developer's Toolkit and PostScript documentation for UNIX,
VMS, Ultrix, AIX, MacOS, DOS, and Microsoft Windows systems is available
in a compressed UNIX tar file by anonymous ftp from 'ftp.ncbi.nih.gov',
in the toolbox/ncbi_tools directory. The file is 'ncbi.tar.Z'.
5. KNOWN PROBLEMS OF THE GENBANK DATABASE
5.1 Incorrect Gene Symbols in Entries and Index
The /gene qualifier for many GenBank entries contains values other than the
official gene symbol, such as the product or the standard name of the gene. The
gene symbol index (gbgen.idx) is created from the data in the /gene qualifier
and therefore may contain data other than official gene symbols.
6. GENBANK ADMINISTRATION
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH GenBank Sequence Database. NCBI distributes
GenBank sequence data by anonymous FTP, e-mail servers and other
network services. For more information, you may contact NCBI at the
e-mail address: [email protected] or by phone: 301-496-2475.
6.1 Registered Trademark Notice
GenBank (R) is a registered trademark of the U.S. Department of Health
and Human Services for the Genetic Sequence Data Bank.
6.2 Citing GenBank
If you have used GenBank in your research, we would appreciate it if
you would include a reference to GenBank in all publications related
to that research.
When citing data in GenBank, it is appropriate to give the sequence
name, primary accession number, and the publication in which the
sequence first appeared. If the data are unpublished, we urge you to
contact the group which submitted the data to GenBank to see if there
is a recent publication or if they have determined any revisions or
extensions of the data.
It is also appropriate to list a reference for GenBank itself. The
following publication, which describes the GenBank database, should
be cited:
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A.,
Wheeler D.L. GenBank. Nucl. Acids Res. 28(1):15-18 (2000)
The following statement is an example of how you may cite GenBank
data. It cites the sequence, its primary accession number, the group
who determined the sequence, and GenBank. The numbers in parentheses
refer to the GenBank citation above and to the REFERENCE in the
GenBank sequence entry.
`We scanned the GenBank (1) database for sequence similarities and
found one sequence (2), GenBank accession number J01016, which showed
significant similarity...'
(1) Benson, D.A. et al. Nucl. Acids Res. 28(1):15-18 (2000)
(2) Nellen, W. and Gallwitz, D. J. Mol. Biol. 159, 1-18 (1982)
6.3 GenBank Distribution Formats and Media
Complete flat file releases of the GenBank database are available via
NCBI's anonymous ftp server:
ftp://ftp.ncbi.nih.gov
Each release is cumulative, incorporating all previous GenBank data.
No retrieval software is provided. GenBank distribution via CD-ROM
ceased as of GenBank Release 106.0 (April, 1998).
Mirrors of the GenBank FTP site at the NCBI are available from the
San Diego Supercomputer Center and the University of Indiana:
ftp://genbank.sdsc.edu/pub
ftp://bio-mirror.net/biomirror/genbank/
6.4 Other Methods of Accessing GenBank Data
Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, 3D structure data, complete genomes,
and associated MEDLINE entries. The system is produced by the National
Center for Biotechnology Information (NCBI), and is available only via
the Internet (using the Web-Entrez and Network-Entrez applications).
Accessing Entrez is easy: if you have a World Wide Web browser, such as
Netscape or Internet-Explorer, simply point your browser to:
http://www.ncbi.nlm.nih.gov/
The Web version of Entrez has all the capabilities of the network version,
but with the visual style of the World Wide Web. If you prefer the "look and
feel" of Network-Entrez, you may download Network-Entrez from the NCBI's
FTP server:
ftp://ftp.ncbi.nih.gov/
Versions are available for PC/Windows, Macintosh and several Unix variants.
For information about Network-Entrez, Web-Entrez or any other NCBI
services, you may contact NCBI by e-mail at [email protected] or by
phone at 301-496-2475.
6.5 Request for Corrections and Comments
We welcome your suggestions for improvements to GenBank. We are
especially interested to learn of errors or inconsistencies in the
data. BankIt or Sequin can be used to submit revisions to previous
submissions. In addition, suggestions and corrections can be sent by
electronic mail to: [email protected]. Please be certain to
indicate the GenBank release number (e.g., Release 135.0) and the
primary accession number of the entry to which your comments apply; it
is helpful if you also give the entry name and the current contents of
any data field for which you are recommending a change.
6.6 Credits and Acknowledgments
Credits -
GenBank Release Coordination
Mark Cavanaugh
GenBank Submission Coordination
Ilene Mizrachi
GenBank Annotation Staff
Lori Black, Larissa Brown, Larry Chlumsky, Karen Clark, Irene Fang,
Michael Fetchko, Anjanette Johnston, Pierre Ledoux, Richard McVeigh,
Leonie Misquitta, Ilene Mizrachi, DeAnne Olsen Cravaritis,
Chris O'Sullivan, David Rasko, Leigh Riley, Gert Roosen, Susan
Schafer, Suh-suh Wang, Jane Weisemann, Steven Wilhite, and
Linda Yankie
Data Management and Preparation
Vladimir Alekseyev, Serge Bazhin, Anton Butanaev, Mark Cavanaugh,
Hsiu-Chuan Chen, Jonathan Kans, Michael Kimelman, Jim Ostell,
Karl Sirotkin, Vladimir Soussov, Elena Starchenko, Hanzhen Sun,
Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann, Eugene Yaschenko
Database Administration
Helen Epting, Slava Khotomliansky, Tony Stearman
User Support
Medha Bhagwat, Peter Cooper, Susan Dombrowski, Andrei Gabrielian
Renata Geer, Scott McGinnis, Donna Messersmith, Rana Morris, Vyvy Pham,
Monica Romiti, Eric Sayers, Tao Tao, David Wheeler
Project Direction
David Lipman
Acknowledgments -
Contractor support for GenBank production and distribution has been
provided by Management Systems Designers, Inc., ComputerCraft Corporation,
and The KEVRIC Company, Inc.
6.7 Disclaimer
The United States Government makes no representations or warranties
regarding the content or accuracy of the information. The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights. The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.
For additional information about GenBank releases, please contact
NCBI by e-mail at [email protected], by phone at (301) 496-2475,
or by mail at:
GenBank
National Library of Medicine
Bldg. 38A Rm. 8N-809
8600 Rockville Pike
Bethesda, MD 20894
FAX: (301) 480-9241
