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OpenFluDB, a database for human and animal influenza virus

Contributors

Liechti, Robin; Gleizes, Anne; Kuznetsov, Dmitry; Bougueleret, Lydie; Le Mercier, Philippe; Bairoch, Amos Marc; Xenarios, Ioannis

Published in

Database, vol. 2010, baq004

Publication date

2010

Abstract

Although research on influenza lasted for more than 100 years, it is still one of the most prominent diseases causing half a million human deaths every year. With the recent observation of new highly pathogenic H5N1 and H7N7 strains, and the appearance of the influenza pandemic caused by the H1N1 swine-like lineage, a collaborative effort to share observations on the evolution of this virus in both animals and humans has been established. The OpenFlu database (OpenFluDB) is a part of this collaborative effort. It contains genomic and protein sequences, as well as epidemiological data from more than 27,000 isolates. The isolate annotations include virus type, host, geographical location and experimentally tested antiviral resistance. Putative enhanced pathogenicity as well as human adaptation propensity are computed from protein sequences. Each virus isolate can be associated with the laboratories that collected, sequenced and submitted it. Several analysis tools including multiple sequence alignment, phylogenetic analysis and sequence similarity maps enable rapid and efficient mining. The contents of OpenFluDB are supplied by direct user submission, as well as by a daily automatic procedure importing data from public repositories. Additionally, a simple mechanism facilitates the export of OpenFluDB records to GenBank. This resource has been successfully used to rapidly and widely distribute the sequences collected during the recent human swine flu outbreak and also as an exchange platform during the vaccine selection procedure. Database URL: http://openflu.vital-it.ch.

Keywords

  • Animals
  • Birds
  • Databases, Genetic
  • Evolution, Molecular
  • Genome, Viral
  • Humans
  • Influenza A Virus, H1N1 Subtype/genetics/isolation & purification
  • Influenza in Birds/virology
  • Influenza, Human/virology
  • Orthomyxoviridae/genetics/isolation & purification
  • Orthomyxoviridae Infections/virology
  • Phylogeny
  • Sequence Alignment/statistics & numerical data
  • Swine
  • User-Computer Interface

UNIGE affiliation entities

UNIGE research groups

Citation (ISO format)

LIECHTI, Robin et al. OpenFluDB, a database for human and animal influenza virus. In: Database, 2010, vol. 2010, p. baq004. doi: 10.1093/database/baq004

Main files (1)

Article (Published version)

Identifiers

Additional URL for this publication

http://openflu.vital-it.ch/

Journal ISSN

1758-0463
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704downloads

Technical informations

Creation

05/05/2014 10:50:00

First validation

05/05/2014 10:50:00

Update

14/03/2023 21:11:12

Status update

14/03/2023 21:11:11

Last indexation

30/10/2024 17:04:59
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