Influenza Virus Resource
presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank,
combined with tools for flu sequence analysis and annotation.
In addition, it provides links to other resources that contain flu sequences,
publications and general information about flu viruses.
|New features added to the Influenza Virus Resource
04/17/2013: The complete genome of a human A (H7N9) isolate has been released in GenBank. It is available at NCBI's Influenza Virus Sequence Database.
04/05/2013: The HA, NA and MP segments of a human A (H7N9) isolate have been released in GenBank. They are available at NCBI's Influenza Virus Sequence Database.
02/15/2013: The Influenza Virus Sequence Annotation Tool is capable of predicting the PA-X protein now.
05/02/2012: The new "Full-length only" and "Full-length plus" features are now available in the
flu database. "Full-length only" applies to sequences that have complete coding regions including start and stop codons, and they are labelled as "c" (for complete) in the database query result.
"Full-length plus" applies to all "Full-length only" sequences, plus those only missing start and/or stop codons, which are labelled as "nc" (for nearly complete) in the database query result. Partial
sequences are labelled as "p" in the database query result.
10/27/2011: The genomic sequence annotation tool also works for Influenza C viruses now.
07/06/2011: The database can now be searched by northern temperate, southern temperate and tropical regions
from the "Country/Region" field,
and the regions (N, S and T) are indicated in the search result.
05/20/2011: Sequences of prototype viruses of well defined lineages/clades can now be selected in the database through "Additional
filters". Currently, this includes those for Influenza
B viruses (Victoria and Yamagata), and the H5N1 and H9N2 subtypes of Influenza A viruses.
01/27/2011: GenBank accession numbers of amino acid sequences in a selected branch of a tree can now be downloaded.
12/01/2010: Sequences of WHO recommended vaccine strains can now be selected in the database through "Additional
06/10/2010: The definition line of the FASTA sequences in the downloaded files can now be customized by users.
05/17/2010: New features were added to the Influenza Virus Resource.
1. Multiple names in the same field (Host, Country etc.) can be selected in the database query page.
2. GenBank sequence release date can be selected.
3. Sequences with month or day in the collection date can be selected/retrieved.
4. It is now possible to retrieve sequences only when selected other segments of the same virus also exist in the database.
11/03/2009: A new design of the Influenza Virus Resource went to public. New features include:
1. Drug-resistance mutations are annotated and searchable in the database.
2. Sequences can be retrieved from the database using multiple GenBank accession numbers.
3. Collapsed identical sequences can be displayed and selected from the database search result.
4. Database search result table can be downloaded in XML, CSV or tab-delimited format.
07/20/2009: Pandemic (H1N1) 2009 virus sequences can now be excluded from the database search results.
06/19/2009: 2009 H1N1 influenza virus sequences can now be retrieved from the database by selecting "Sequences from Pandemic (H1N1) 2009 virus only".
04/27/2009: The first 40 2009 H1N1 influenza virus sequences are available
03/25/2009: Month and day can now be included in addition to year as collection date in the database
search queries. Please note that
not all sequences have month and day available. Therefore sequences with only year as collection date will not be included
in a search if a month of the corresponding year is entered in the query. For example, a search for sequences from
2006/05 to 2008/11 will retrieve those with month in collection date for 2006 and 2008, but not those with only 2006 or 2008
as collection date (because they could be from 2006/04 or 2008/12). However, all sequences from 2007, with or without month in the collection date, will be included in such
11/04/2008: Proteins belong to segments that encode more than one protein (e.g. M1 and M2) can now be searched separately from the database.
01/30/2008: Phylogenetic trees created by the tree tool can now be exported in the Newick format to be displayed by other tree-viewing programs.
01/03/2008: A manuscript entitled The Influenza Virus Resource at the National Center for
Biotechnology Information is published in Journal of Virology.
10/17/2007: A manuscript entitled The Influenza Virus Resource at the National Center for Biotechnology Information is accepted by the Journal of Virology.
10/05/2007: The signature mutation, E627K, in the PB2 protein (e.g. AY651719) that might confer high virulence of influenza viruses can be detected and reported by the genome annotation tool now.
08/20/2007: An improved multiple sequence alignment tool and a new
version of the tree building tool are
available now. In the multiple sequence alignment result, the anchor/consensus sequence can be displayed for copying.
The printer-friendly output of the multiple sequence alignment shows virus strain names in addition to accession numbers
of the sequences. The tree building tool can take up to 1,000 sequences and has the ability to change the resolutions
of branches of interest on the tree. Sequences on the tree can be searched by the fields in the database, and the resulting sequences or groups will be highlighted.
07/11/2007: A new version of the tree building tool is
available for testing. It can take up to 1000 sequences and has the ability to expand branches of interest on the tree.
06/01/2007: A paper describing the web tool for flu genome annotation is
published online in Nucleic Acids Research.
05/14/2007: An option to remove identical sequences in a dataset is available now.
05/11/2007: Some of the signature mutations that might confer drug resistance by influenza viruses can be detected and reported by the genome annotation tool now. Such mutations include V27A and S31N in the M2 protein, H274Y and R292K in the N1 subtype of neuraminidase, and N294S in the N2 subtype of neuraminidase.
02/08/2007: The genome annotation tool can take multiple sequences
as an input now.
12/22/2006: Full-length nucleotide and protein sequences are flagged in the influenza_na.dat and influenza_aa.dat files in ftp.
11/22/2006: Daily updates of the NCBI Influenza Virus Sequence Database are now available in the "updates" directory through ftp.
10/04/2006: The genomic sequence annotation tool also works for Influenza B viruses now.
06/22/2006: A web tool for flu genomic sequence annotation is now available.
05/12/2006: Genomes of the same virus isolate but sequenced in different labs are now identified and grouped
separately in the database.
04/28/2006: In the multiple sequence alignment of coding regions, non-synonymous changes (in triplets) are now highlighted in a different background color.
04/25/2006: The consensus sequence in the multiple sequence alignment can now be replaced with a sequence of your
04/19/2006: A nucleotide/protein sequence (e.g. AGCGAAAGCAGGGGT or RSKV) can now be added to the "Search by a string" box to be included
in the database search.
03/28/2006: The multiple sequence alignment is now shown in its intact in a scrollable window, and a printer-friendly version of the
alignment is now available.
03/20/2006: An advanced database search tool is now available.
03/09/2006: In the FASTA sequences downloaded from the database, the following string is inserted between the GenBank sequence identifier and the sequence title in the FASTA definition lines: /host/segment number(name)/subtype/country/year/month/date/.
02/13/2006: A list of GenBank accession numbers for selected protein or nucleotide sequences can now be downloaded from the database.
12/14/2005: Continents have been added to the Country/Region field in the database.
11/17/2005: The new design of the Influenza Virus Resource went to public.
10/19/2005: Data in the NCBI Influenza Virus Sequence Database are now available through ftp.
11/17/2004: The Influenza Virus Resource was first launched.