Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.ncbi.nlm.nih.gov/genomes/FLU/
Full name: NCBI Influenza Virus Resource
Description: NCBI Influenza Virus Sequence Database helps users to build queries, retrieve sequences, find complete genome sets, do multiple sequence alignment, and build clustering or phylogenetic trees.
Year founded: 2008
Last update: 2017-1
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
DNA
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: National Center for Biotechnology Information
Address: 8600 Rockville Pike,Bethesda,MD 20894,USA
City: Bethesda
Province/State: MD
Country/Region: United States
Contact name (PI/Team): Influenza Virus team
Contact email (PI/Helpdesk): info@ncbi.nlm.nih.gov

Publications

17942553
The influenza virus resource at the National Center for Biotechnology Information. [PMID: 17942553]
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D.
J Virol. 2008:82(2) | 573 Citations (from Europe PMC, 2021-06-19)
18485197
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. [PMID: 18485197]
Zaslavsky L, Bao Y, Tatusova TA.

With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval. We developed an approach to visualize large phylogenetic trees in an aggregated form with a special representation of subscale details. The initial aggregated tree representation is built with a level of resolution automatically selected to fit into the available screen space, with terminal groups selected based on sequence similarity. The default aggregated representation can be refined by users interactively.Structure and data variability within terminal groups are displayed using small trees that have the same vertical size as the text annotation of the group. These subscale representations are calculated using systematic sampling from the corresponding terminal group. The aggregated tree containing terminal groups can be annotated using aggregation of structured metadata, such as seasonal distribution, geographic locations, etc. The algorithms are implemented in JavaScript within the NCBI Influenza Virus Resource 1.

BMC Bioinformatics. 2008:9() | 14 Citations (from Europe PMC, 2021-06-19)
17545199
FLAN: a web server for influenza virus genome annotation. [PMID: 17545199]
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Tatusova T.

FLAN (short for FLu ANnotation), the NCBI web server for genome annotation of influenza virus (http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi) is a tool for user-provided influenza A virus or influenza B virus sequences. It can validate and predict protein sequences encoded by an input flu sequence. The input sequence is BLASTed against a database containing influenza sequences to determine the virus type (A or B), segment (1 through 8) and subtype for the hemagglutinin and neuraminidase segments of influenza A virus. For each segment/subtype of the viruses, a set of sample protein sequences is maintained. The input sequence is then aligned against the corresponding protein set with a 'Protein to nucleotide alignment tool' (ProSplign). The translated product from the best alignment to the sample protein sequence is used as the predicted protein encoded by the input sequence. The output can be a feature table that can be used for sequence submission to GenBank (by Sequin or tbl2asn), a GenBank flat file, or the predicted protein sequences in FASTA format. A message showing the length of the input sequence, the predicted virus type, segment and subtype for the hemagglutinin and neuraminidase segments of Influenza A virus will also be displayed.

Nucleic Acids Res. 2007:35(Web Server issue) | 28 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
204/5061 (95.989%)
Health and medicine:
43/1067 (96.064%)
Gene genome and annotation:
80/1350 (94.148%)
204
Total Rank
615
Citations
43.929
z-index

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Record metadata

Created on: 2017-09-08
Curated by:
Lina Ma [2019-04-21]
Lina Ma [2018-06-08]
Lina Ma [2017-09-08]