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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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GenBank.

Eric W Sayers1, Mark Cavanaugh1, Karen Clark1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Nucleic Acids Research
|October 27, 2018
PubMed
Summary
This summary is machine-generated.

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GenBank is a vital public database for nucleotide sequences from over 420,000 species. It ensures worldwide coverage through daily data exchange and offers integrated access to related biological information and search tools.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • GenBank is a comprehensive public repository for nucleotide sequences.
  • It archives data from diverse sources, including individual labs and large-scale sequencing projects.
  • Global data sharing is facilitated through daily exchange with ENA and DDBJ.

Purpose of the Study:

  • To describe the GenBank database, its submission methods, and data accessibility.
  • To highlight recent updates and enhancements to the GenBank resource.
  • To emphasize GenBank's role in the broader biological research community.

Main Methods:

  • Data acquisition through submission portals (BankIt, tbl2asn) and large-scale projects.
  • Daily data synchronization with the European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ).

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  • Integration with NCBI Nucleotide database for access to related genomic and biomedical information.

    • Main Results:

    • GenBank contains publicly available nucleotide sequences for 420,000 described species.
    • The database is accessible via the NCBI Nucleotide database, linking to taxonomy, genomes, proteins, and literature.
    • Sequence similarity searches are enabled by BLAST, and data is available via FTP.

    Conclusions:

    • GenBank is a crucial, continuously updated resource for genomic data.
    • Recent updates enhance its capacity and usability for researchers.
    • Its integration with other NCBI resources and global databases solidifies its central role in biological research.