The GenBank Submissions Handbook

This book contains information on GenBank, the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

Contents

• GenBank Submission Resources Quick Start
  Created: April 6, 2011; Last Update: November 3, 2014.
  • What Kind of Data Can be Submitted to GenBank?
    Created: April 6, 2011; Last Update: November 3, 2014.
  • Before Starting the Submission Process
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Choosing the Appropriate Submission Resource
    • Learn about GenBank Records before you Submit
  • Submitting Sequences using Specific NCBI Submission Tools
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Submission using BankIt
    • Submission using Sequin
    • Submission using tbl2asn
  • Submitting Different Sequence Types using Specific NCBI Submission Resources
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Submission to the Transcriptome Shotgun Assembly Sequence database (TSA)
    • Submission to the High-Throughput Genomic (HTG) sequence division of GenBank
    • Submission of Full Length Insert cDNA (FLIC) Submissions
    • Genome Submissions
    • Submission of Third Party Annotation Records
    • Submission to the database of Expressed Sequence Tags (dbEST)
    • Submission to the database of Genome Survey Sequences (dbGSS)
  • Submitting Multiple Sequences as a Set
    Created: April 6, 2011; Last Update: November 3, 2014.
  • Adding Value to your Submission
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Information to include with Genomic Sequence Submissions
    • Information to include with RNA/mRNA Sequence Submissions
  • Formatting your Submission
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Sequence Formatting
    • Making Tab-delimited Tables
  • Annotating your Sequence for Submission
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Why Should I Add Features to my Sequence?
    • Feature Annotation Using BankIt
    • Feature Annotation Using Sequin
  • Providing Source Information in your Submission
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Source information for Samples Collected in the Field
    • Eukaryotic Source Material
    • Bacterial and Archaeal Source Material
    • Viral Source Material
    • Museum/Reference Collection Source Material
    • How to Describe Unknown Source Material in Your Submission
  • Setting Release Dates for your Submission
    Created: April 6, 2011; Last Update: November 3, 2014.
  • Sending your Submission to GenBank
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Problems Sending Files by email
  • Submission Processing
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Time Required to Process Submission
    • Acknowledgement of Submission
    • Accession Numbers
  • Changing a File or Record after Submission (Submission Updates)
    Created: April 6, 2011; Last Update: November 3, 2014.
    • Changing (Updating) a Record Using Sequin
    • Update Not from Original Submitter
• A User’s Guide to BankIt
  Michael Fetchko and Adrienne Kitts.
  • The Design of this User’s Guide
    Michael Fetchko and Adrienne Kitts.
  • What is BankIt?
    Michael Fetchko and Adrienne Kitts.
    • BankIt’s Multi Page Tab Design
    • Messages from the BankIt Program
    • Questions about using BankIt
  • The “Contact” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • New Submitters
    • Users with an existing BankIt Account
    • Alternate Email Addresses
    • Common Mistakes Made While Filling out the Contact Page
  • The “Reference” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • The “Sequence Authors” Section
    • The “Reference Information” Section
    • Common Mistakes Made While Filling Out the “Reference” Page
  • The “Nucleotide” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • The “Submission Release Date” Section
    • The “16S rRNA Submissions” Section
    • The “Sequence(s) and Definition Line(s)”Section
    • Common Mistakes Made While Filling Out the “Nucleotide” Page
  • The “Organism” Page
    Michael Fetchko and Adrienne Kitts.
  • The “Set/Batch” Page
    Michael Fetchko and Adrienne Kitts.
  • The “Submission Category” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • Original Submissions
    • Third Party Annotation (TPA)
    • Common Mistakes Made While Filling Out the “Submission Category” Page
  • The “Source Modifiers” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • Bacterial/Archaeal Sequences
    • Mouse and Rat Submissions
    • Rice Submissions
    • Virus Submissions
    • The “Source Information” Section
    • The “Source Modifiers” Section
    • Common Mistakes Made While Filling Out the “Source Modifiers” Page
  • The “Primers” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • Single Sequence Submissions
    • Multiple Sequence Submissions
    • Common Mistakes Made While Filling Out the “Primers” Page
  • The “Features” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • Adding Features to your Sequence: Feature Table File vs. Online BankIt Forms
    • Adding Features by Uploading a Feature Table
    • Adding Features using the Online BankIt Forms
    • Common Mistakes Made While Filling Out the “Features” Page
  • The “Review and Correct” Page
    Michael Fetchko and Adrienne Kitts.
    • Purpose
    • Correspondence
    • If You Have Been Asked to Resubmit Your Sequence(s)
    • Additional Text Descriptions of your Sequence
    • Additional/Corrected Source Modifier/Feature Tables
    • Reviewing your Submission
    • Submitting Your Sequence
  • After Submission
    Michael Fetchko and Adrienne Kitts.
    • Submission Processing
    • Contacting GenBank about a Submission you have made
    • Accessing your Submission File Once you Submit
    • Updating your Submission
• A User’s Guide to the Sequin Wizards
  Created: May 15, 2012; Last Update: January 16, 2014.
  • The Design of this User’s Guide
    Created: May 15, 2012; Last Update: January 16, 2014.
  • What are the Sequin Wizards?
    Created: May 15, 2012; Last Update: January 16, 2014.
  • How do you access the Wizards?
    Created: May 15, 2012; Last Update: January 16, 2014.
  • Submission Wizard for Viruses
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Submission Type
    • Virus Wizard Type of Virus
    • Virus Wizard Source Information
    • Norovirus, Sapovirus (Caliciviridae) Requirements
    • Foot-and-mouth Disease Virus Requirements
    • Influenza Virus Requirements
    • Rotavirus Requirements
    • Not listed above or mixed set of different viruses Requirements
    • Virus Wizard Molecule Information
    • Virus Wizard Annotation
  • Submission Wizard for Uncultured Samples
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Submission Type
    • Uncultured Sample Wizard Source Information
    • Uncultured Sample Wizard Primer Type
    • Uncultured Sample Annotation
    • Wizard rRNA Chimera Checking
  • Submission Wizard for rRNA-ITS-IGS Sequences
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Submission Type
    • rRNA-ITS-IGS Wizard Type of Source
    • rRNA-ITS-IGS Wizard Source Information
    • rRNA-ITS-IGS Wizard Genome
    • rRNA-ITS-IGS Wizard Annotation
    • Wizard rRNA Chimera Checking
  • Submission Wizard for Intergenic Spacer (IGS) Sequences
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Submission Type
    • IGS Wizard Type of Source
    • IGS Wizard Source Information
    • IGS Wizard Genome
    • IGS Wizard Annotation
  • Submission Wizard for Microsatellite sequences
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Microsatellite Wizard Molecule Type
    • Microsatellite Wizard Annotation
    • Microsatellite Wizard Information
  • Submission Wizard for D-loops and Control Regions
    Created: May 15, 2012; Last Update: January 16, 2014.
    • Purpose
    • Wizard Import Nucleotide Sequences
    • Sequencing Method
    • Submission Type
    • D-Loop Wizard Source Information
    • D-Loop Wizard Annotation
    • D-Loop Wizard Features
    • D-Loop Wizard Feature Annotation
• Glossary
  Created: April 6, 2011.