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Database Commons - NCBI Influenza Virus Resource

NCBI Influenza Virus Resource

Citations: 842

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Short name NCBI Influenza Virus Resource
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.
URL http://www.ncbi.nlm.nih.gov/genomes/FLU/
Year founded 2008
Last update & version     
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address 8600 Rockville Pike,Bethesda,MD 20894,USA
City Bethesda
Province/State MD
Country/Region United States
Contact name Yiming Bao
Contact email bao@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • influenza virus sequence
Publication(s)
  • Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. [PMID: 18485197]

    Leonid Zaslavsky, Yiming Bao, Tatiana A Tatusova
    BMC bioinformatics 2008:9
    21 Citations (Google Scholar as of 2017-09-08)

    Abstract: 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.

  • The influenza virus resource at the National Center for Biotechnology Information. [PMID: 17942553]

    Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Leonid Zaslavsky, Tatiana Tatusova, Jim Ostell, David Lipman
    Journal of virology 2008:82(2)
    789 Citations (Google Scholar as of 2017-09-08)

    Abstract:

  • FLAN: a web server for influenza virus genome annotation. [PMID: 17545199]

    Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Tatiana Tatusova
    Nucleic acids research 2007:35(Web Server issue)
    32 Citations (Google Scholar as of 2017-09-08)

    Abstract: 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.

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-1 Failed2017-09-08

Tags

Disease DNA
Influenza virus
influenza virus sequence

Record metadata

  • Created on: 2017-09-08
  • Curated by:
    • Lina Ma [2017-09-08]
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