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Publicly available genome sequence database for viruses?

Bioinformatics Asked by AlwaysTrying44 on May 30, 2021

As a small introductory project, I want to compare genome sequences of different strains of influenza virus.

What are the publicly available databases of influenza virus gene/genome sequences?

3 Answers

There area few different influenza virus database resources:

  • The Influenza Research Database (IRD) (a.k.a FluDB - based upon URL)
    • A NIAID Bioinformatics Resource Center or BRC which highly curates the data brought in and integrates it with numerous other relevant data types
  • The NCBI Influenza Virus Resource
    • A sub-project of the NCBI with data curated over and above the GenBank data that is part of the NCBI
  • The GISAID EpiFlu Database
    • A database of sequences from the Global Initiative on Sharing All Influenza Data. Has unique data from many countries but requires user agree to a data sharing policy.
  • The OpenFluDB
    • Former GISAID database that contains some sequence data that GenBank does not have.

For those who also may be interested in other virus databases, there are:

  • Virus Pathogen Resource (VIPR)
    • A companion portal to the IRD, which hosts curated and integrated data for most other NIAID A-C virus pathogens including (but not limited to) Ebola, Zika, Dengue, Enterovirus, and Hepatitis C
  • LANL HIV database
    • Los Alamos National Laboratory HIV database with HIV data and many useful tools for all virus bioinformatics
  • PaVE: Papilloma virus genome database (from quintik comment)
    • NIAID developed and maintained Papilloma virus bioinformatics portal

Disclaimer: I used to work for the IRD / VIPR and currently work for NIAID.

Correct answer by burkesquires on May 30, 2021

Answered by GenoMax on May 30, 2021

In addition to what others have suggested, I would also recommend PaVE as a resource. This is a curated database maintained by the NIAID and current holds over 300 papilloma virus genomes.

Answered by quantik on May 30, 2021

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