Release Notes For GenBank Release 129
GBREL.TXT Genetic Sequence Data Bank
April 15 2002
NCBI-GenBank Flat File Release 129.0
Distribution Release Notes
16769983 loci, 19072679701 bases, from 16769983 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 129.0
1.2 Cutoff Date
1.3 Important Changes in Release 129.0
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
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1. INTRODUCTION
1.1 Release 129.0
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 129.0 is a release of sequence data by NCBI in the GenBank
flat file 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. Sequence data is also incorporated from the Genome Sequence Data Base
(GSDB), Santa Fe, NM. 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, 129.0, incorporates data available to the collaborating
databases as of April 22, 2002. 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 Network-Entrez or Web-Entrez applications to query interactively
the Entrez: Nucleotides database (see Section 6.4 of this document).
o Use the NCBI 'query' email server to search the GenBank Updates. Instructions
regarding the use of the e-mail server can be obtained by sending an email
message with the word 'help' in it to: [email protected]
1.3 Important Changes in Release 129.0
1.3.1 Organizational changes
Due to database growth, the EST division is now being split into 161 pieces.
Due to database growth, the GSS division is now being split into 51 pieces.
Due to database growth, the HTG division is now being split into 33 pieces.
Due to database growth, the PRI division is now being split into 19 pieces.
Due to database growth, the ROD division is now being split into 3 pieces.
Due to database growth, the VRL division is now being split into 3 pieces.
1.3.2 New REFERENCE type for on-line journals
Agreement was reached at the May 1999 collaborative DDBJ/EMBL/GenBank
meeting that an effort should be made to accomodate references which are
published only on-line. Until specifications for such references are
available from library organizations, GenBank will begin to present them in
the following manner, as of this April 2002 GenBank Release :
REFERENCE 1 (bases 1 to 2858)
AUTHORS Smith, J.
TITLE Cloning and expression of a phospholipase gene
JOURNAL Online Publication
REMARK Online-Journal-name; Article Identifier; URL
1.3.3 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 eight
GSS flatfiles in Release 129.0. Consider the gbgss44.seq file:
GBGSS1.SEQ Genetic Sequence Data Bank
April 15 2002
NCBI-GenBank Flat File Release 129
GSS Sequences (Part 1)
Here, the filename and part number in the header is "1", though the file
has been renamed as "44" based on the files dumped from the other system.
We will work to resolve this discrepancy in future releases, but the priority
is admittedly much lower than many other tasks.
1.4 Upcoming Changes
1.4.1 New CONSRTM linetype for references.
In order to capture the names of consortia and other groups that are involved
in large-scale sequencing projects, a new linetype called CONSRTM will become
legal in the REFERENCE block of the GenBank flatfile format as of June, 2002 .
Consider, for example, the literature citation associated with PubMed
identifier 11237011 :
Nature 2001 Feb 15;409(6822):860-921
Initial sequencing and analysis of the human genome.
In addition to the very long list of author names, a consortium is associated
with this publication:
International Human Genome Sequencing Consortium
With the addition of a CONSRTM linetype, collective names like this will
have a dedicated location in the flatfile format. Records which currently
attempt to force consortium names into the last entry of the AUTHORS line
will be updated to utilize the new linetype.
Note that multiple consortia for a REFERENCE may exist, in which case
they will be separated by a semi-colon. It is also possible that references
with a CONSRTM linetype will not have any individual AUTHORS at all.
1.4.2 Selenocysteine representation
Selenocysteine residues within the protein translations of coding
region features have been represented in GenBank via the letter 'X'
and a /transl_except qualifier. At the May 1999 DDBJ/EMBL/GenBank
collaborative meeting, it was learned that IUPAC plans to adopt the
letter 'U' for selenocysteine.
DDBJ, EMBL, and GenBank will thus use this new amino acid abbreviation
for its /translation qualifiers. Although a timetable for its appearance
has not been finalized, we are mentioning this now because the introduction
of a new residue abbreviation is a fairly fundamental change.
Details about the use of 'U' will be made available via these release
notes and the GenBank newsgroup as they become available.
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 296 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. gbjou.idx - Index of the entries according to journal citation.
17. gbgen.idx - Index of the entries according to gene names.
18. gbsec.idx - Index of the entries according to secondary accession number.
19. gbpri1.seq - Primate sequence entries, part 1.
20. gbpri2.seq - Primate sequence entries, part 2.
21. gbpri3.seq - Primate sequence entries, part 3.
22. gbpri4.seq - Primate sequence entries, part 4.
23. gbpri5.seq - Primate sequence entries, part 5.
24. gbpri6.seq - Primate sequence entries, part 6.
25. gbpri7.seq - Primate sequence entries, part 7.
26. gbpri8.seq - Primate sequence entries, part 8.
27. gbpri9.seq - Primate sequence entries, part 9.
28. gbpri10.seq - Primate sequence entries, part 10.
29. gbpri11.seq - Primate sequence entries, part 11.
30. gbpri12.seq - Primate sequence entries, part 12.
31. gbpri13.seq - Primate sequence entries, part 13.
32. gbpri14.seq - Primate sequence entries, part 14.
33. gbpri15.seq - Primate sequence entries, part 15.
34. gbpri16.seq - Primate sequence entries, part 16.
35. gbpri17.seq - Primate sequence entries, part 17.
36. gbpri18.seq - Primate sequence entries, part 18.
37. gbpri19.seq - Primate sequence entries, part 19.
38. gbrod1.seq - Rodent sequence entries, part 1.
39. gbrod2.seq - Rodent sequence entries, part 2.
40. gbrod3.seq - Rodent sequence entries, part 3.
41. gbmam.seq - Other mammalian sequence entries.
42. gbvrt.seq - Other vertebrate sequence entries.
43. gbinv1.seq - Invertebrate sequence entries, part 1.
44. gbinv2.seq - Invertebrate sequence entries, part 2.
45. gbinv3.seq - Invertebrate sequence entries, part 3.
46. gbinv4.seq - Invertebrate sequence entries, part 4.
47. gbinv5.seq - Invertebrate sequence entries, part 5.
48. gbpln1.seq - Plant sequence entries (including fungi and algae), part 1.
49. gbpln2.seq - Plant sequence entries (including fungi and algae), part 2.
50. gbpln3.seq - Plant sequence entries (including fungi and algae), part 3.
51. gbpln4.seq - Plant sequence entries (including fungi and algae), part 4.
52. gbpln5.seq - Plant sequence entries (including fungi and algae), part 5.
53. gbbct1.seq - Bacterial sequence entries, part 1.
54. gbbct2.seq - Bacterial sequence entries, part 2.
55. gbbct3.seq - Bacterial sequence entries, part 3.
56. gbbct4.seq - Bacterial sequence entries, part 4.
57. gbbct5.seq - Bacterial sequence entries, part 5.
58. gbvrl1.seq - Viral sequence entries, part 1.
59. gbvrl2.seq - Viral sequence entries, part 2.
60. gbvrl3.seq - Viral sequence entries, part 3.
61. gbphg.seq - Phage sequence entries.
62. gbsyn.seq - Synthetic and chimeric sequence entries.
63. gbuna.seq - Unannotated sequence entries.
64. gbest1.seq - EST (expressed sequence tag) sequence entries, part 1.
65. gbest2.seq - EST (expressed sequence tag) sequence entries, part 2.
66. gbest3.seq - EST (expressed sequence tag) sequence entries, part 3.
67. gbest4.seq - EST (expressed sequence tag) sequence entries, part 4.
68. gbest5.seq - EST (expressed sequence tag) sequence entries, part 5.
69. gbest6.seq - EST (expressed sequence tag) sequence entries, part 6.
70. gbest7.seq - EST (expressed sequence tag) sequence entries, part 7.
71. gbest8.seq - EST (expressed sequence tag) sequence entries, part 8.
72. gbest9.seq - EST (expressed sequence tag) sequence entries, part 9.
73. gbest10.seq - EST (expressed sequence tag) sequence entries, part 10.
74. gbest11.seq - EST (expressed sequence tag) sequence entries, part 11.
75. gbest12.seq - EST (expressed sequence tag) sequence entries, part 12.
76. gbest13.seq - EST (expressed sequence tag) sequence entries, part 13.
77. gbest14.seq - EST (expressed sequence tag) sequence entries, part 14.
78. gbest15.seq - EST (expressed sequence tag) sequence entries, part 15.
79. gbest16.seq - EST (expressed sequence tag) sequence entries, part 16.
80. gbest17.seq - EST (expressed sequence tag) sequence entries, part 17.
81. gbest18.seq - EST (expressed sequence tag) sequence entries, part 18.
82. gbest19.seq - EST (expressed sequence tag) sequence entries, part 19.
83. gbest20.seq - EST (expressed sequence tag) sequence entries, part 20.
84. gbest21.seq - EST (expressed sequence tag) sequence entries, part 21.
85. gbest22.seq - EST (expressed sequence tag) sequence entries, part 22.
86. gbest23.seq - EST (expressed sequence tag) sequence entries, part 23.
87. gbest24.seq - EST (expressed sequence tag) sequence entries, part 24.
88. gbest25.seq - EST (expressed sequence tag) sequence entries, part 25.
89. gbest26.seq - EST (expressed sequence tag) sequence entries, part 26.
90. gbest27.seq - EST (expressed sequence tag) sequence entries, part 27.
91. gbest28.seq - EST (expressed sequence tag) sequence entries, part 28.
92. gbest29.seq - EST (expressed sequence tag) sequence entries, part 29.
93. gbest30.seq - EST (expressed sequence tag) sequence entries, part 30.
94. gbest31.seq - EST (expressed sequence tag) sequence entries, part 31.
95. gbest32.seq - EST (expressed sequence tag) sequence entries, part 32.
96. gbest33.seq - EST (expressed sequence tag) sequence entries, part 33.
97. gbest34.seq - EST (expressed sequence tag) sequence entries, part 34.
98. gbest35.seq - EST (expressed sequence tag) sequence entries, part 35.
99. gbest36.seq - EST (expressed sequence tag) sequence entries, part 36.
100. gbest37.seq - EST (expressed sequence tag) sequence entries, part 37.
101. gbest38.seq - EST (expressed sequence tag) sequence entries, part 38.
102. gbest39.seq - EST (expressed sequence tag) sequence entries, part 39.
103. gbest40.seq - EST (expressed sequence tag) sequence entries, part 40.
104. gbest41.seq - EST (expressed sequence tag) sequence entries, part 41.
105. gbest42.seq - EST (expressed sequence tag) sequence entries, part 42.
106. gbest43.seq - EST (expressed sequence tag) sequence entries, part 43.
107. gbest44.seq - EST (expressed sequence tag) sequence entries, part 44.
108. gbest45.seq - EST (expressed sequence tag) sequence entries, part 45.
109. gbest46.seq - EST (expressed sequence tag) sequence entries, part 46.
110. gbest47.seq - EST (expressed sequence tag) sequence entries, part 47.
111. gbest48.seq - EST (expressed sequence tag) sequence entries, part 48.
112. gbest49.seq - EST (expressed sequence tag) sequence entries, part 49.
113. gbest50.seq - EST (expressed sequence tag) sequence entries, part 50.
114. gbest51.seq - EST (expressed sequence tag) sequence entries, part 51.
115. gbest52.seq - EST (expressed sequence tag) sequence entries, part 52.
116. gbest53.seq - EST (expressed sequence tag) sequence entries, part 53.
117. gbest54.seq - EST (expressed sequence tag) sequence entries, part 54.
118. gbest55.seq - EST (expressed sequence tag) sequence entries, part 55.
119. gbest56.seq - EST (expressed sequence tag) sequence entries, part 56.
120. gbest57.seq - EST (expressed sequence tag) sequence entries, part 57.
121. gbest58.seq - EST (expressed sequence tag) sequence entries, part 58.
122. gbest59.seq - EST (expressed sequence tag) sequence entries, part 59.
123. gbest60.seq - EST (expressed sequence tag) sequence entries, part 60.
124. gbest61.seq - EST (expressed sequence tag) sequence entries, part 61.
125. gbest62.seq - EST (expressed sequence tag) sequence entries, part 62.
126. gbest63.seq - EST (expressed sequence tag) sequence entries, part 63.
127. gbest64.seq - EST (expressed sequence tag) sequence entries, part 64.
128. gbest65.seq - EST (expressed sequence tag) sequence entries, part 65.
129. gbest66.seq - EST (expressed sequence tag) sequence entries, part 66.
130. gbest67.seq - EST (expressed sequence tag) sequence entries, part 67.
131. gbest68.seq - EST (expressed sequence tag) sequence entries, part 68.
132. gbest69.seq - EST (expressed sequence tag) sequence entries, part 69.
133. gbest70.seq - EST (expressed sequence tag) sequence entries, part 70.
134. gbest71.seq - EST (expressed sequence tag) sequence entries, part 71.
135. gbest72.seq - EST (expressed sequence tag) sequence entries, part 72.
136. gbest73.seq - EST (expressed sequence tag) sequence entries, part 73.
137. gbest74.seq - EST (expressed sequence tag) sequence entries, part 74.
138. gbest75.seq - EST (expressed sequence tag) sequence entries, part 75.
139. gbest76.seq - EST (expressed sequence tag) sequence entries, part 76.
140. gbest77.seq - EST (expressed sequence tag) sequence entries, part 77.
141. gbest78.seq - EST (expressed sequence tag) sequence entries, part 78.
142. gbest79.seq - EST (expressed sequence tag) sequence entries, part 79.
143. gbest80.seq - EST (expressed sequence tag) sequence entries, part 80.
144. gbest81.seq - EST (expressed sequence tag) sequence entries, part 81.
145. gbest82.seq - EST (expressed sequence tag) sequence entries, part 82.
146. gbest83.seq - EST (expressed sequence tag) sequence entries, part 83.
147. gbest84.seq - EST (expressed sequence tag) sequence entries, part 84.
148. gbest85.seq - EST (expressed sequence tag) sequence entries, part 85.
149. gbest86.seq - EST (expressed sequence tag) sequence entries, part 86.
150. gbest87.seq - EST (expressed sequence tag) sequence entries, part 87.
151. gbest88.seq - EST (expressed sequence tag) sequence entries, part 88.
152. gbest89.seq - EST (expressed sequence tag) sequence entries, part 89
153. gbest90.seq - EST (expressed sequence tag) sequence entries, part 90.
154. gbest91.seq - EST (expressed sequence tag) sequence entries, part 91.
155. gbest92.seq - EST (expressed sequence tag) sequence entries, part 92.
156. gbest93.seq - EST (expressed sequence tag) sequence entries, part 93.
157. gbest94.seq - EST (expressed sequence tag) sequence entries, part 94.
158. gbest95.seq - EST (expressed sequence tag) sequence entries, part 95.
159. gbest96.seq - EST (expressed sequence tag) sequence entries, part 96.
160. gbest97.seq - EST (expressed sequence tag) sequence entries, part 97.
161. gbest98.seq - EST (expressed sequence tag) sequence entries, part 98.
162. gbest99.seq - EST (expressed sequence tag) sequence entries, part 99.
163. gbest100.seq - EST (expressed sequence tag) sequence entries, part 100.
164. gbest101.seq - EST (expressed sequence tag) sequence entries, part 101.
165. gbest102.seq - EST (expressed sequence tag) sequence entries, part 102.
166. gbest103.seq - EST (expressed sequence tag) sequence entries, part 103.
167. gbest104.seq - EST (expressed sequence tag) sequence entries, part 104.
168. gbest105.seq - EST (expressed sequence tag) sequence entries, part 105.
169. gbest106.seq - EST (expressed sequence tag) sequence entries, part 106.
170. gbest107.seq - EST (expressed sequence tag) sequence entries, part 107.
171. gbest108.seq - EST (expressed sequence tag) sequence entries, part 108.
172. gbest109.seq - EST (expressed sequence tag) sequence entries, part 109.
173. gbest110.seq - EST (expressed sequence tag) sequence entries, part 110.
174. gbest111.seq - EST (expressed sequence tag) sequence entries, part 111.
175. gbest112.seq - EST (expressed sequence tag) sequence entries, part 112.
176. gbest113.seq - EST (expressed sequence tag) sequence entries, part 113.
177. gbest114.seq - EST (expressed sequence tag) sequence entries, part 114.
178. gbest115.seq - EST (expressed sequence tag) sequence entries, part 115.
179. gbest116.seq - EST (expressed sequence tag) sequence entries, part 116.
180. gbest117.seq - EST (expressed sequence tag) sequence entries, part 117.
181. gbest118.seq - EST (expressed sequence tag) sequence entries, part 118.
182. gbest119.seq - EST (expressed sequence tag) sequence entries, part 119.
183. gbest120.seq - EST (expressed sequence tag) sequence entries, part 120.
184. gbest121.seq - EST (expressed sequence tag) sequence entries, part 121.
185. gbest122.seq - EST (expressed sequence tag) sequence entries, part 122.
186. gbest123.seq - EST (expressed sequence tag) sequence entries, part 123.
187. gbest124.seq - EST (expressed sequence tag) sequence entries, part 124.
188. gbest125.seq - EST (expressed sequence tag) sequence entries, part 125.
189. gbest126.seq - EST (expressed sequence tag) sequence entries, part 126.
190. gbest127.seq - EST (expressed sequence tag) sequence entries, part 127.
191. gbest128.seq - EST (expressed sequence tag) sequence entries, part 128.
192. gbest129.seq - EST (expressed sequence tag) sequence entries, part 129.
193. gbest130.seq - EST (expressed sequence tag) sequence entries, part 130.
194. gbest131.seq - EST (expressed sequence tag) sequence entries, part 131.
195. gbest132.seq - EST (expressed sequence tag) sequence entries, part 132.
196. gbest133.seq - EST (expressed sequence tag) sequence entries, part 133.
197. gbest134.seq - EST (expressed sequence tag) sequence entries, part 134.
198. gbest135.seq - EST (expressed sequence tag) sequence entries, part 135.
199. gbest136.seq - EST (expressed sequence tag) sequence entries, part 136.
200. gbest137.seq - EST (expressed sequence tag) sequence entries, part 137.
201. gbest138.seq - EST (expressed sequence tag) sequence entries, part 138.
202. gbest139.seq - EST (expressed sequence tag) sequence entries, part 139.
203. gbest140.seq - EST (expressed sequence tag) sequence entries, part 140.
204. gbest141.seq - EST (expressed sequence tag) sequence entries, part 141.
205. gbest142.seq - EST (expressed sequence tag) sequence entries, part 142.
206. gbest143.seq - EST (expressed sequence tag) sequence entries, part 143.
207. gbest144.seq - EST (expressed sequence tag) sequence entries, part 144.
208. gbest145.seq - EST (expressed sequence tag) sequence entries, part 145.
209. gbest146.seq - EST (expressed sequence tag) sequence entries, part 146.
210. gbest147.seq - EST (expressed sequence tag) sequence entries, part 147.
211. gbest148.seq - EST (expressed sequence tag) sequence entries, part 148.
212. gbest149.seq - EST (expressed sequence tag) sequence entries, part 149.
213. gbest150.seq - EST (expressed sequence tag) sequence entries, part 150.
214. gbest151.seq - EST (expressed sequence tag) sequence entries, part 151.
215. gbest152.seq - EST (expressed sequence tag) sequence entries, part 152.
216. gbest153.seq - EST (expressed sequence tag) sequence entries, part 153.
217. gbest154.seq - EST (expressed sequence tag) sequence entries, part 154.
218. gbest155.seq - EST (expressed sequence tag) sequence entries, part 155.
219. gbest156.seq - EST (expressed sequence tag) sequence entries, part 156.
220. gbest157.seq - EST (expressed sequence tag) sequence entries, part 157.
221. gbest158.seq - EST (expressed sequence tag) sequence entries, part 158.
222. gbest159.seq - EST (expressed sequence tag) sequence entries, part 159.
223. gbest160.seq - EST (expressed sequence tag) sequence entries, part 160.
224. gbest161.seq - EST (expressed sequence tag) sequence entries, part 161.
225. gbpat1.seq - Patent sequence entries, part 1.
226. gbpat2.seq - Patent sequence entries, part 2.
227. gbpat3.seq - Patent sequence entries, part 3.
228. gbpat4.seq - Patent sequence entries, part 4.
229. gbsts1.seq - STS (sequence tagged site) sequence entries, part 1.
230. gbsts2.seq - STS (sequence tagged site) sequence entries, part 2.
231. gbgss1.seq - GSS (genome survey sequence) sequence entries, part 1.
232. gbgss2.seq - GSS (genome survey sequence) sequence entries, part 2.
233. gbgss3.seq - GSS (genome survey sequence) sequence entries, part 3.
234. gbgss4.seq - GSS (genome survey sequence) sequence entries, part 4.
235. gbgss5.seq - GSS (genome survey sequence) sequence entries, part 5.
236. gbgss6.seq - GSS (genome survey sequence) sequence entries, part 6.
237. gbgss7.seq - GSS (genome survey sequence) sequence entries, part 7.
238. gbgss8.seq - GSS (genome survey sequence) sequence entries, part 8.
239. gbgss9.seq - GSS (genome survey sequence) sequence entries, part 9.
240. gbgss10.seq - GSS (genome survey sequence) sequence entries, part 10.
241. gbgss11.seq - GSS (genome survey sequence) sequence entries, part 11.
242. gbgss12.seq - GSS (genome survey sequence) sequence entries, part 12.
243. gbgss13.seq - GSS (genome survey sequence) sequence entries, part 13.
244. gbgss14.seq - GSS (genome survey sequence) sequence entries, part 14.
245. gbgss15.seq - GSS (genome survey sequence) sequence entries, part 15.
246. gbgss16.seq - GSS (genome survey sequence) sequence entries, part 16.
247. gbgss17.seq - GSS (genome survey sequence) sequence entries, part 17.
248. gbgss18.seq - GSS (genome survey sequence) sequence entries, part 18.
249. gbgss19.seq - GSS (genome survey sequence) sequence entries, part 19.
250. gbgss20.seq - GSS (genome survey sequence) sequence entries, part 20.
251. gbgss21.seq - GSS (genome survey sequence) sequence entries, part 21.
252. gbgss22.seq - GSS (genome survey sequence) sequence entries, part 22.
253. gbgss23.seq - GSS (genome survey sequence) sequence entries, part 23.
254. gbgss24.seq - GSS (genome survey sequence) sequence entries, part 24.
255. gbgss25.seq - GSS (genome survey sequence) sequence entries, part 25.
256. gbgss26.seq - GSS (genome survey sequence) sequence entries, part 26.
257. gbgss27.seq - GSS (genome survey sequence) sequence entries, part 27.
258. gbgss28.seq - GSS (genome survey sequence) sequence entries, part 28.
259. gbgss29.seq - GSS (genome survey sequence) sequence entries, part 29.
260. gbgss30.seq - GSS (genome survey sequence) sequence entries, part 30.
261. gbgss31.seq - GSS (genome survey sequence) sequence entries, part 31.
262. gbgss32.seq - GSS (genome survey sequence) sequence entries, part 32.
263. gbgss33.seq - GSS (genome survey sequence) sequence entries, part 33.
264. gbgss34.seq - GSS (genome survey sequence) sequence entries, part 34.
265. gbgss35.seq - GSS (genome survey sequence) sequence entries, part 35.
266. gbgss36.seq - GSS (genome survey sequence) sequence entries, part 36.
267. gbgss37.seq - GSS (genome survey sequence) sequence entries, part 37.
268. gbgss38.seq - GSS (genome survey sequence) sequence entries, part 38.
269. gbgss39.seq - GSS (genome survey sequence) sequence entries, part 39.
270. gbgss40.seq - GSS (genome survey sequence) sequence entries, part 40.
271. gbgss41.seq - GSS (genome survey sequence) sequence entries, part 41.
272. gbgss42.seq - GSS (genome survey sequence) sequence entries, part 42.
273. gbgss43.seq - GSS (genome survey sequence) sequence entries, part 43.
274. gbgss44.seq - GSS (genome survey sequence) sequence entries, part 44.
275. gbgss45.seq - GSS (genome survey sequence) sequence entries, part 45.
276. gbgss46.seq - GSS (genome survey sequence) sequence entries, part 46.
277. gbgss47.seq - GSS (genome survey sequence) sequence entries, part 47.
278. gbgss48.seq - GSS (genome survey sequence) sequence entries, part 48.
279. gbgss49.seq - GSS (genome survey sequence) sequence entries, part 49.
280. gbgss50.seq - GSS (genome survey sequence) sequence entries, part 50.
281. gbgss51.seq - GSS (genome survey sequence) sequence entries, part 51.
282. gbhtg1.seq - HTGS (high throughput genomic sequencing) sequence entries, part 1.
283. gbhtg2.seq - HTGS (high throughput genomic sequencing) sequence entries, part 2.
284. gbhtg3.seq - HTGS (high throughput genomic sequencing) sequence entries, part 3.
285. gbhtg4.seq - HTGS (high throughput genomic sequencing) sequence entries, part 4.
286. gbhtg5.seq - HTGS (high throughput genomic sequencing) sequence entries, part 5.
287. gbhtg6.seq - HTGS (high throughput genomic sequencing) sequence entries, part 6.
288. gbhtg7.seq - HTGS (high throughput genomic sequencing) sequence entries, part 7.
289. gbhtg8.seq - HTGS (high throughput genomic sequencing) sequence entries, part 8.
290. gbhtg9.seq - HTGS (high throughput genomic sequencing) sequence entries, part 9.
291. gbhtg10.seq - HTGS (high throughput genomic sequencing) sequence entries, part 10.
292. gbhtg11.seq - HTGS (high throughput genomic sequencing) sequence entries, part 11.
293. gbhtg12.seq - HTGS (high throughput genomic sequencing) sequence entries, part 12.
294. gbhtg13.seq - HTGS (high throughput genomic sequencing) sequence entries, part 13.
295. gbhtg14.seq - HTGS (high throughput genomic sequencing) sequence entries, part 14.
296. gbhtg15.seq - HTGS (high throughput genomic sequencing) sequence entries, part 15.
297. gbhtg16.seq - HTGS (high throughput genomic sequencing) sequence entries, part 16.
298. gbhtg17.seq - HTGS (high throughput genomic sequencing) sequence entries, part 17.
299. gbhtg18.seq - HTGS (high throughput genomic sequencing) sequence entries, part 18.
300. gbhtg19.seq - HTGS (high throughput genomic sequencing) sequence entries, part 19.
301. gbhtg20.seq - HTGS (high throughput genomic sequencing) sequence entries, part 20.
302. gbhtg21.seq - HTGS (high throughput genomic sequencing) sequence entries, part 21.
303. gbhtg22.seq - HTGS (high throughput genomic sequencing) sequence entries, part 22.
304. gbhtg23.seq - HTGS (high throughput genomic sequencing) sequence entries, part 23.
305. gbhtg24.seq - HTGS (high throughput genomic sequencing) sequence entries, part 24.
306. gbhtg25.seq - HTGS (high throughput genomic sequencing) sequence entries, part 25.
307. gbhtg26.seq - HTGS (high throughput genomic sequencing) sequence entries, part 26.
308. gbhtg27.seq - HTGS (high throughput genomic sequencing) sequence entries, part 27.
309. gbhtg28.seq - HTGS (high throughput genomic sequencing) sequence entries, part 28.
310. gbhtg29.seq - HTGS (high throughput genomic sequencing) sequence entries, part 29.
311. gbhtg30.seq - HTGS (high throughput genomic sequencing) sequence entries, part 30.
312. gbhtg31.seq - HTGS (high throughput genomic sequencing) sequence entries, part 31.
313. gbhtg32.seq - HTGS (high throughput genomic sequencing) sequence entries, part 32.
314. gbhtg33.seq - HTGS (high throughput genomic sequencing) sequence entries, part 33.
315. gbhtc.seq - HTC (high throughput cDNA sequencing) entries.
Three supplemental files provide the accession numbers of GenBank entries
that are new, updated, or deleted since the previous release:
a. gbchg.txt - Entries updated since the previous release.
b. gbdel.txt - Entries deleted since the previous release.
c. gbnew.txt - Entries new since the previous release.
An experimental file called gbcon.seq provides an alternative representation
for complex sequences, such as "segmented sets" and complete-genomes that have
been split into pieces. The GenBank README describes the experimental CON
division of GenBank in more detail:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
2.2.5 File Sizes
Uncompressed, the Release 129.0 flatfiles require roughly 66.43 GB (sequence
files only) or 74.72 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
546075172 gbacc.idx
505202340 gbaut1.idx
517749450 gbaut10.idx
441655380 gbaut11.idx
509825238 gbaut2.idx
501262350 gbaut3.idx
500000795 gbaut4.idx
504806540 gbaut5.idx
512648554 gbaut6.idx
500049572 gbaut7.idx
511433848 gbaut8.idx
502456074 gbaut9.idx
250020730 gbbct1.seq
250001857 gbbct2.seq
250000149 gbbct3.seq
250003263 gbbct4.seq
65651295 gbbct5.seq
2755180 gbchg.txt
27847 gbdel.txt
230690037 gbest1.seq
230690177 gbest10.seq
230689375 gbest100.seq
230689844 gbest101.seq
230688702 gbest102.seq
230298195 gbest103.seq
229425956 gbest104.seq
230687904 gbest105.seq
230687579 gbest106.seq
230688010 gbest107.seq
230687600 gbest108.seq
230688907 gbest109.seq
230689299 gbest11.seq
230689839 gbest110.seq
230689449 gbest111.seq
230687539 gbest112.seq
230689781 gbest113.seq
230687906 gbest114.seq
230689164 gbest115.seq
230688706 gbest116.seq
230688594 gbest117.seq
230687788 gbest118.seq
230688652 gbest119.seq
230687593 gbest12.seq
230690186 gbest120.seq
230689962 gbest121.seq
230688026 gbest122.seq
230689603 gbest123.seq
230689661 gbest124.seq
230689199 gbest125.seq
230687813 gbest126.seq
230688986 gbest127.seq
230689432 gbest128.seq
230688615 gbest129.seq
230688012 gbest13.seq
230687633 gbest130.seq
230690399 gbest131.seq
230688522 gbest132.seq
230687945 gbest133.seq
230689392 gbest134.seq
230689082 gbest135.seq
230688023 gbest136.seq
230688311 gbest137.seq
230689625 gbest138.seq
230691269 gbest139.seq
230688159 gbest14.seq
230691275 gbest140.seq
230687946 gbest141.seq
230689452 gbest142.seq
230689108 gbest143.seq
230689199 gbest144.seq
230690108 gbest145.seq
230690284 gbest146.seq
230689677 gbest147.seq
230688186 gbest148.seq
230691120 gbest149.seq
230689291 gbest15.seq
230690055 gbest150.seq
230689193 gbest151.seq
230689246 gbest152.seq
230687765 gbest153.seq
230689121 gbest154.seq
230688743 gbest155.seq
230690034 gbest156.seq
230690303 gbest157.seq
230689604 gbest158.seq
222068412 gbest159.seq
230690648 gbest16.seq
230689952 gbest160.seq
228754063 gbest161.seq
230689381 gbest17.seq
230689433 gbest18.seq
230687542 gbest19.seq
230408502 gbest2.seq
230688299 gbest20.seq
230689113 gbest21.seq
230690388 gbest22.seq
230690697 gbest23.seq
230689983 gbest24.seq
230690350 gbest25.seq
230689043 gbest26.seq
230687630 gbest27.seq
230690200 gbest28.seq
230687570 gbest29.seq
230689666 gbest3.seq
230688910 gbest30.seq
230688080 gbest31.seq
230689328 gbest32.seq
216976910 gbest33.seq
190977502 gbest34.seq
193755382 gbest35.seq
217226196 gbest36.seq
216152452 gbest37.seq
216102447 gbest38.seq
216875925 gbest39.seq
230687645 gbest4.seq
230688363 gbest40.seq
230689840 gbest41.seq
221451342 gbest42.seq
230687848 gbest43.seq
230688997 gbest44.seq
230688873 gbest45.seq
230687645 gbest46.seq
230687703 gbest47.seq
230689292 gbest48.seq
230689629 gbest49.seq
163939285 gbest5.seq
230690309 gbest50.seq
230689771 gbest51.seq
230688524 gbest52.seq
230689594 gbest53.seq
230688626 gbest54.seq
230688996 gbest55.seq
229935890 gbest56.seq
230689058 gbest57.seq
225362984 gbest58.seq
209582361 gbest59.seq
181532829 gbest6.seq
208879568 gbest60.seq
208636970 gbest61.seq
209125908 gbest62.seq
210342239 gbest63.seq
209352115 gbest64.seq
208119596 gbest65.seq
209752893 gbest66.seq
210091724 gbest67.seq
205476725 gbest68.seq
207080375 gbest69.seq
230689161 gbest7.seq
207591910 gbest70.seq
208587171 gbest71.seq
217602105 gbest72.seq
230689937 gbest73.seq
230689393 gbest74.seq
229390215 gbest75.seq
214794889 gbest76.seq
213053286 gbest77.seq
216908837 gbest78.seq
230687671 gbest79.seq
230689378 gbest8.seq
230687596 gbest80.seq
230688596 gbest81.seq
230688412 gbest82.seq
230688897 gbest83.seq
230688286 gbest84.seq
230690316 gbest85.seq
230688463 gbest86.seq
230688702 gbest87.seq
230690006 gbest88.seq
230689949 gbest89.seq
230690427 gbest9.seq
230689210 gbest90.seq
230689392 gbest91.seq
230689218 gbest92.seq
230687862 gbest93.seq
230689516 gbest94.seq
230688442 gbest95.seq
230688967 gbest96.seq
230689451 gbest97.seq
230691265 gbest98.seq
230688881 gbest99.seq
20397431 gbgen.idx
209716673 gbgss1.seq
209716580 gbgss10.seq
209716260 gbgss11.seq
209716769 gbgss12.seq
209718544 gbgss13.seq
209717291 gbgss14.seq
209718371 gbgss15.seq
209715988 gbgss16.seq
209717008 gbgss17.seq
209718383 gbgss18.seq
209718425 gbgss19.seq
209716102 gbgss2.seq
209718203 gbgss20.seq
209716501 gbgss21.seq
209719589 gbgss22.seq
209716179 gbgss23.seq
209717858 gbgss24.seq
209719159 gbgss25.seq
209718032 gbgss26.seq
209716387 gbgss27.seq
209717221 gbgss28.seq
209717083 gbgss29.seq
209718114 gbgss3.seq
209716836 gbgss30.seq
209716421 gbgss31.seq
209716068 gbgss32.seq
209716266 gbgss33.seq
209716531 gbgss34.seq
209716801 gbgss35.seq
209716889 gbgss36.seq
209718457 gbgss37.seq
209718038 gbgss38.seq
209717095 gbgss39.seq
209718028 gbgss4.seq
209718555 gbgss40.seq
209716401 gbgss41.seq
209717109 gbgss42.seq
53451126 gbgss43.seq
250002706 gbgss44.seq
250000011 gbgss45.seq
250000964 gbgss46.seq
250003217 gbgss47.seq
250001763 gbgss48.seq
250002787 gbgss49.seq
209716965 gbgss5.seq
250001534 gbgss50.seq
147656200 gbgss51.seq
209716541 gbgss6.seq
209716635 gbgss7.seq
209718414 gbgss8.seq
209718559 gbgss9.seq
169011343 gbhtc.seq
250002604 gbhtg1.seq
250167846 gbhtg10.seq
250081160 gbhtg11.seq
250207044 gbhtg12.seq
250121304 gbhtg13.seq
250071153 gbhtg14.seq
250008330 gbhtg15.seq
250095068 gbhtg16.seq
250131899 gbhtg17.seq
250094767 gbhtg18.seq
250116997 gbhtg19.seq
250058307 gbhtg2.seq
250014680 gbhtg20.seq
250025788 gbhtg21.seq
250018994 gbhtg22.seq
250189438 gbhtg23.seq
250091533 gbhtg24.seq
250233222 gbhtg25.seq
250119254 gbhtg26.seq
250156927 gbhtg27.seq
250020739 gbhtg28.seq
250112408 gbhtg29.seq
250162414 gbhtg3.seq
250049818 gbhtg30.seq
250087340 gbhtg31.seq
250050827 gbhtg32.seq
232770079 gbhtg33.seq
250165035 gbhtg4.seq
250101618 gbhtg5.seq
250025049 gbhtg6.seq
250008334 gbhtg7.seq
250123667 gbhtg8.seq
250222479 gbhtg9.seq
250080350 gbinv1.seq
250005380 gbinv2.seq
250005793 gbinv3.seq
250000171 gbinv4.seq
62930345 gbinv5.seq
488889583 gbjou.idx
379728008 gbkey.idx
124325028 gbmam.seq
20348004 gbnew.txt
250000567 gbpat1.seq
250002541 gbpat2.seq
250000873 gbpat3.seq
190644566 gbpat4.seq
17453564 gbphg.seq
250000485 gbpln1.seq
250000599 gbpln2.seq
250001980 gbpln3.seq
250075837 gbpln4.seq
184364440 gbpln5.seq
250024323 gbpri1.seq
250030034 gbpri10.seq
250070026 gbpri11.seq
250010925 gbpri12.seq
250019233 gbpri13.seq
250208526 gbpri14.seq
250001377 gbpri15.seq
250132895 gbpri16.seq
250000771 gbpri17.seq
250005747 gbpri18.seq
171814573 gbpri19.seq
250042097 gbpri2.seq
250197404 gbpri3.seq
250120762 gbpri4.seq
250043052 gbpri5.seq
250072560 gbpri6.seq
250014249 gbpri7.seq
250116491 gbpri8.seq
250051218 gbpri9.seq
115655 gbrel.txt
250206475 gbrod1.seq
250002741 gbrod2.seq
84180176 gbrod3.seq
134161813 gbsdr.txt
1281941 gbsec.idx
250000460 gbsts1.seq
72529844 gbsts2.seq
30805120 gbsyn.seq
1401880 gbuna.seq
250002684 gbvrl1.seq
250001589 gbvrl2.seq
16018267 gbvrl3.seq
243829185 gbvrt.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 18304 103702046
BCT2 46962 94865361
BCT3 25403 102133037
BCT4 35350 93373870
BCT5 13213 24058125
EST1 68773 26545772
EST10 76874 29906577
EST100 71027 37675749
EST101 70442 45757685
EST102 77060 34945134
EST103 75022 27916560
EST104 76207 26099686
EST105 73997 41449259
EST106 67026 33128783
EST107 79270 50111691
EST108 79919 45589922
EST109 72920 45771962
EST11 76745 29137247
EST110 69712 42735598
EST111 73541 47883909
EST112 68483 44615634
EST113 73626 44914285
EST114 78061 45177405
EST115 72405 49583936
EST116 75508 48234060
EST117 76616 47709159
EST118 78032 33106652
EST119 79129 32272702
EST12 77244 30897406
EST120 80473 47621334
EST121 75416 42872096
EST122 65300 35511215
EST123 73946 38315030
EST124 69177 40192080
EST125 66338 36057030
EST126 72246 43784415
EST127 72817 44564585
EST128 68225 39501971
EST129 74187 41268472
EST13 78722 30401539
EST130 71065 44082918
EST131 63333 39217068
EST132 78153 42489515
EST133 102889 56996459
EST134 80158 43271446
EST135 108462 57223134
EST136 93420 54230156
EST137 67370 35814543
EST138 65872 30615827
EST139 57234 28888617
EST14 79017 31589426
EST140 62781 31047381
EST141 60313 30760649
EST142 67674 35500360
EST143 73586 52082822
EST144 65489 44686167
EST145 82879 48894609
EST146 58601 29939135
EST147 63042 32136056
EST148 67627 40496249
EST149 67374 39825192
EST15 73159 31047300
EST150 62804 40994438
EST151 74995 40897139
EST152 65396 44754302
EST153 95994 37641129
EST154 109865 38963125
EST155 74029 26040777
EST156 73116 27097847
EST157 74359 26377573
EST158 73006 26497367
EST159 78455 26422019
EST16 75572 33117590
EST160 72744 29124142
EST161 74358 28251692
EST17 85372 34392440
EST18 79095 32474941
EST19 81635 33973443
EST2 75524 28992456
EST20 72957 29578237
EST21 72781 33612084
EST22 77348 30802883
EST23 76686 31815373
EST24 75905 34707944
EST25 73547 30923483
EST26 76044 31247758
EST27 80583 36179968
EST28 83001 42232507
EST29 76294 62119067
EST3 74271 30174902
EST30 87747 50914348
EST31 103009 48161992
EST32 97889 50305437
EST33 84721 33131050
EST34 69405 18533128
EST35 72103 19524885
EST36 56199 17221384
EST37 43634 11904573
EST38 43147 11899553
EST39 43118 11369500
EST4 74696 28150982
EST40 86993 36748140
EST41 96570 44262795
EST42 90905 47518714
EST43 85959 40377512
EST44 106539 56599673
EST45 92587 44476463
EST46 75347 31861592
EST47 69102 30715052
EST48 71419 30968172
EST49 74191 31217784
EST5 48621 15381716
EST50 83262 32871614
EST51 71838 28090419
EST52 64763 29310564
EST53 74558 32234660
EST54 74820 35259156
EST55 76806 33703833
EST56 74514 25992516
EST57 81794 32867790
EST58 66694 28182180
EST59 40120 11363822
EST6 56835 18519864
EST60 40260 11730093
EST61 40457 12615641
EST62 40655 12276541
EST63 40599 12683509
EST64 40603 12791656
EST65 40563 12266467
EST66 40279 12343217
EST67 40520 12429527
EST68 41366 12075938
EST69 41283 12756873
EST7 74831 29464448
EST70 41209 13027427
EST71 41113 13147369
EST72 44497 12147635
EST73 42385 22336347
EST74 41478 23569452
EST75 43938 18078706
EST76 50509 23088276
EST77 51772 21465213
EST78 53483 21739401
EST79 76025 32577342
EST8 76996 30943639
EST80 74222 29572664
EST81 74559 32719818
EST82 77477 46327018
EST83 78476 41175924
EST84 76728 39597367
EST85 78782 39201579
EST86 71496 41845208
EST87 74335 32646155
EST88 75737 41051143
EST89 71389 35299462
EST9 78054 30171213
EST90 78118 50497948
EST91 65640 34471399
EST92 72312 37173050
EST93 74659 44874345
EST94 73504 43751563
EST95 71516 42945793
EST96 74904 39741561
EST97 70625 30995025
EST98 67265 31941403
EST99 66500 38969533
GSS1 83934 35983236
GSS10 67041 35998094
GSS11 70629 39711333
GSS12 61939 32354027
GSS13 68344 35531620
GSS14 68329 34807380
GSS15 66062 29672635
GSS16 64261 31970705
GSS17 72704 43558868
GSS18 65755 30767142
GSS19 57765 26812693
GSS2 83798 36237477
GSS20 52357 27204271
GSS21 53009 25506487
GSS22 53987 22986771
GSS23 59547 37882577
GSS24 57229 26658904
GSS25 53433 25475901
GSS26 64468 41354731
GSS27 60906 24413080
GSS28 53786 23467218
GSS29 60120 29489327
GSS3 83165 38791543
GSS30 62142 30365126
GSS31 64559 35950683
GSS32 81792 36223282
GSS33 69550 37351212
GSS34 66426 41784200
GSS35 67203 38172493
GSS36 74194 37329570
GSS37 70362 37480383
GSS38 76022 42789714
GSS39 86247 57278891
GSS4 75075 38549398
GSS40 85729 55672831
GSS41 80974 43080131
GSS42 79914 44453358
GSS43 20927 9154859
GSS44 84330 64382427
GSS45 81028 60806354
GSS46 81982 65791173
GSS47 76621 63789887
GSS48 74611 63003311
GSS49 66552 64688072
GSS50 86830 54795745
GSS51 58207 25873791
GSS5 72281 38653019
GSS6 70389 35250127
GSS7 72399 36335319
GSS8 71867 36782226
GSS9 68981 34212049
HTC 24688 32587397
HTG1 1294 191116621
HTG10 1280 188549011
HTG11 1082 191310005
HTG12 1344 188729068
HTG13 1459 187787555
HTG14 1190 191154874
HTG15 1352 184472564
HTG16 1430 185071889
HTG17 1474 185532979
HTG18 1963 180354713
HTG19 2259 175178637
HTG2 1757 189570950
HTG20 1631 185128642
HTG21 1361 185596584
HTG22 1382 185633800
HTG23 1564 184109746
HTG24 1547 182861157
HTG25 1643 184265110
HTG26 1622 184145687
HTG27 1809 182837012
HTG28 1675 183512599
HTG29 1223 191865233
HTG3 2676 187371292
HTG30 1030 194353997
HTG31 1053 193598818
HTG32 1262 191068609
HTG33 1215 178439544
HTG4 2192 189924802
HTG5 2209 189529417
HTG6 1304 188477462
HTG7 1228 188765946
HTG8 1244 188722919
HTG9 1225 188962134
INV1 7679 178665420
INV2 5977 164456393
INV3 69805 79195797
INV4 30397 119922816
INV5 9608 29807606
MAM 38579 40437316
PAT1 222846 70205773
PAT2 151989 84948509
PAT3 116290 111850006
PAT4 129294 49423723
PHG 2031 6682639
PLN1 22667 137038289
PLN2 77066 78587348
PLN3 17977 139388857
PLN4 62727 79535930
PLN5 32884 75158092
PRI1 10757 159813985
PRI10 33825 134587294
PRI11 17637 148301846
PRI12 1571 179274266
PRI13 1749 180407226
PRI14 2220 186592010
PRI15 15596 156606840
PRI16 17194 158861870
PRI17 39629 128743510
PRI18 33342 128476983
PRI19 41926 67084484
PRI2 1391 174029963
PRI3 1301 184407038
PRI4 1183 173412067
PRI5 1157 176958235
PRI6 1224 179072788
PRI7 1297 168807549
PRI8 1378 176185898
PRI9 1417 173353418
ROD1 25838 146817032
ROD2 31709 136351480
ROD3 23953 28043992
STS1 86703 35190051
STS2 30577 11701811
SYN 6804 12648688
UNA 667 330581
VRL1 74997 62887775
VRL2 74742 66698004
VRL3 3353 5750746
VRT 72625 78959948
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 129.0 (chloroplast and mitochon-
drial sequences not included):
Entries Bases Species
5601283 8623240944 Homo sapiens
3588915 2954595785 Mus musculus
407545 1741736289 Rattus norvegicus
331346 675223629 Drosophila melanogaster
305886 318277639 Arabidopsis thaliana
72664 223326041 Oryza sativa (japonica cultivar-group)
197991 221490064 Caenorhabditis elegans
299850 195242860 Brassica oleracea
137414 190743748 Oryza sativa
189090 168566491 Tetraodon nigroviridis
160373 153731744 Pan troglodytes
244485 143288192 Danio rerio
238832 122702872 Bos taurus
256123 118077717 Glycine max
247110 111304151 Zea mays
201305 102882494 Xenopus laevis
155256 95745650 Anopheles gambiae
174486 91194491 Ciona intestinalis
162001 84127124 Lycopersicon esculentum
144094 84096583 Dictyostelium discoideum
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
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, each of the 296 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 2002
NCBI-GenBank Flat File Release 129.0
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 four subkeywords and may repeat. Mandatory
keyword/one or more records.
AUTHORS - Lists the authors of the citation. Mandatory
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/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/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 129.0) 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
Tanya Barrett, Lori Black, Larissa Brown, Larry Chlumsky, Karen
Clark, Irene Fang, Michael Fetchko, Belinda Jackson, Anjanette
Johnston, Dione Kampa, Pierre Ledoux, Richard McVeigh, Leonie
Misquitta, Ilene Mizrachi, DeAnne Olsen Cravaritis, Quy Phung,
David Rasko, Leigh Riley, Paola Roncaglia, 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,
Joel Plotkin, Karl Sirotkin, Vladimir Soussov, Elena Starchenko,
Tatiana Tatusov, Carolyn Tolstoshev, Jane Weisemann, Eugene Yaschenko
Database Administration
Helen Epting, Slava Khotomliansky, Tony Stearman
User Support
Nancy Allmang, Medha Bhagwat, Peter Cooper, Susan Dombrowski,
Renata Geer, Dawn Lipshultz, Eugenia Posey-Marcos, Scott McGinnis,
Vyvy Pham, Barbara Rapp, Monica Romiti, Tao Tao, Rose Marie Woodsmall,
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
