Submitting a Sequence to GenBank

Wei‐Jen Chang1, Kassandra E. Zaila1, Thomas W. Coppola1

1 Hamilton College, Clinton, New York
Publication Name:  Current Protocols Essential Laboratory Techniques
Unit Number:  Unit 11.2
DOI:  10.1002/9780470089941.et1102s12
Online Posting Date:  May, 2016
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Abstract

In the post‐genomic era, more and more research projects involve the generation of molecular sequence data. How should these newly obtained DNA/protein sequences be analyzed, and how should they be prepared for submission to sequence databases? In this unit, we provide guidelines and a flowchart to help first‐time users process new sequence data using third‐party freeware programs and give a step‐by‐step demonstration on the preparation of a sequence file for submission to GenBank using the Sequin program. © 2016 by John Wiley & Sons, Inc.

Keywords: annotation; BankIt; bioedit; bioinformatics; BLAST; jalview; NGS; Sequin

     
 
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Table of Contents

  • Overview and Principles
  • Strategic Planning
  • Basic Protocol 1: Submitting a Novel Sequence to GenBank
  • Basic Protocol 2: Updating an Existing GenBank Record
  • Commentary
  • Figures
     
 
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Materials

Basic Protocol 1: Submitting a Novel Sequence to GenBank

  Materials
  • Computer running Sequin (see Strategic Planning)
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Figures

Videos

Literature Cited

Literature Cited
  Baxevanis, A.D. 2004. An overview of gene identification: Approaches, strategies, and considerations. Curr. Protoc. Bioinform. 6:4.1.1‐4.1.9. doi: 10.1002/0471250953.bi0401s6.
  Benson, D.A., Clark, K., Karsch‐Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W., 2015. GenBank. Nucleic Acids Res. 43, D30‐5. doi: 10.1093/nar/gku1216.
  Hall, T.A. 1999. BioEdit: A user‐friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95‐98. doi: 10.1021/bk‐1999‐0734.ch008.
  Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., and Higgins, D.G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947‐2948. doi: 10.1093/bioinformatics/btm404.
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  Stover, N. A. and Cavalcanti, A. R. 2014. Using NCBI BLAST. Curr. Protoc. Essen. Lab. Tech. 11:11.1.1‐11.1.35.
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  Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., and Barton, G.J., 2009. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189‐1191. doi: 10.1093/bioinformatics/btp033.
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Internet Resources
  http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
  Conserved domain database (CDD; Marchler‐Bauer et al., ). Search for conserved motifs on your protein sequences.
  http://www.ncbi.nlm.nih.gov/
  National Center for Biotechnology Information (NCBI) homepage. Gateway linked to numerous useful resources, such as GenBank, BLAST, and Entrez, among others.
  http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm
  Sequin quick guide. Get detailed information on how to use Sequin.
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