Abstract
GenBank® is a comprehensive database of publicly available DNA sequences for 300,000 named organisms, more than 110,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure and domain information, as well as the biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. GenBank usage scenarios ranging from local analyses of the data available via FTP to online analyses supported by the NCBI web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at www.ncbi.nlm.nih.gov.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2014) GenBank. Nucleic Acids Res 42:D32–D37
Pakseresht N, Alako B, Amid C, Cerdeno-Tarraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S et al (2014) Assembly information services in the European Nucleotide Archive. Nucleic Acids Res 42:D38–D43
Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y (2014) DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res 42:D44–D49
NCBI Resource Coordinators (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 42:D7–D17
Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Res 40:D136–D143
Kodama Y, Shumway M, Leinonen R (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40:D54–D56
Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt KD, Resenchuk S, Tatusova T et al (2012) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res 40:D57–D63
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M et al (2013) NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res 41:D991–D995
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G et al (2013) DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res 41:D936–D941
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311
Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR et al (2012) MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res 40:D461–D464
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR et al (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39:D225–D229
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA et al (2012) PubChem’s BioAssay Database. Nucleic Acids Res 40:D400–D412
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37:W623–W633
Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y et al (2013) BLAST: a more efficient report with usability improvements. Nucleic Acids Res 41:W29–W33
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9
Ye J, McGinnis S, Madden TL (2006) BLAST: improvements for better sequence analysis. Nucleic Acids Res 34:W6–W9
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schaffer AA (2008) Database indexing for production MegaBLAST searches. Bioinformatics 24:1757–1764
Acknowledgements
Funding for this work was provided by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Sayers, E.W., Karsch-Mizrachi, I. (2016). Using GenBank. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3167-5_1
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3166-8
Online ISBN: 978-1-4939-3167-5
eBook Packages: Springer Protocols