Abstract
GenBank® and the Sequence Read Archive (SRA) are comprehensive databases of publicly available DNA sequences. GenBank contains data for 480,000 named organisms, more than 176,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. SRA contains reads from next-generation sequencing studies from over 110,000 species. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage for both databases. GenBank and SRA data are accessible through the NCBI Entrez retrieval system that integrates these data with other data at NCBI, such as genomes, taxonomy, and the biomedical literature. 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. Usage scenarios for both GenBank and SRA ranging from local and cloud analyses to online analyses supported by the NCBI web-based tools are discussed. Both GenBank and SRA, along with their related retrieval and analysis services, are available from the NCBI homepage at www.ncbi.nlm.nih.gov.
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Funding for this work was provided by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.
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Sayers, E.W., O’Sullivan, C., Karsch-Mizrachi, I. (2022). Using GenBank and SRA. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_1
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DOI: https://doi.org/10.1007/978-1-0716-2067-0_1
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