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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?

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  • $\begingroup$ I assume you mean genome sequences rather than gene sequences? $\endgroup$ Jun 7 '17 at 19:40
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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.

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    $\begingroup$ Glad that my upvote allowed you to expand your answer with more links :) I hear ViralZone viralzone.expasy.org is decent too (although I have not used it myself) $\endgroup$ Jun 7 '17 at 18:05
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    $\begingroup$ Thanks Chris! I agree Viral Zone is GREAT! I think it is one of the best virus education site around! $\endgroup$ Jun 7 '17 at 18:13
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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.

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    $\begingroup$ To avoid single link answers, it would be better to suggest edit to burkesquires answer. $\endgroup$
    – zx8754
    Jun 7 '17 at 21:14
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    $\begingroup$ Hi quantik, thanks for your answer and welcome to Bioinformatics Stack Exchange. As a new user with reputation under 50 it's not possible yet for you to comment on other questions or answers (as @zx8754 has recommended), so in this case your answer was the most appropriate thing to do. If you want to improve on someone else's answer in the interim, feel free to edit your answer and incorporate a summary of the other answer(s) that you think are appropriate, making sure to include attribution where appropriate. $\endgroup$
    – gringer
    Jun 7 '17 at 22:18
  • $\begingroup$ Thanks quantik...nice addition. A woeful oversight on my part as I am part of the group that develops PaVE. :-) $\endgroup$ Jun 9 '17 at 1:40
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Influenza virus resource at NCBI or FluDB.

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    $\begingroup$ To avoid single link answers, it would be better to suggest edit to burkesquires answer. $\endgroup$
    – zx8754
    Jun 7 '17 at 21:14
  • $\begingroup$ These are both included above. FluDB is actually the NIAID Influenza Research Database (IRD) Bioinformatics Resource Center (BRC) that has fludb.org as a URL. $\endgroup$ Oct 12 '18 at 16:21

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