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The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA - PLoS Comput. Biol. (2014)

Bottom Line: The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it.Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature.The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.

ABSTRACT
Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

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HIV Mutation Browser interface for Vpu residue 51 showing the navigation, protein and residue panels.(1) Options bar for the residue view section of the interface. (2) Mutation information. (3) User feedback buttons. (4) Mutation information download links. (5) Ancillary residue information panel.
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pcbi-1003951-g003: HIV Mutation Browser interface for Vpu residue 51 showing the navigation, protein and residue panels.(1) Options bar for the residue view section of the interface. (2) Mutation information. (3) User feedback buttons. (4) Mutation information download links. (5) Ancillary residue information panel.

Mentions: The web interface is organised in three panels: the navigation panel at the top; the protein panel in the middle; and the residue panel at the bottom (Figure 3).


The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA - PLoS Comput. Biol. (2014)

HIV Mutation Browser interface for Vpu residue 51 showing the navigation, protein and residue panels.(1) Options bar for the residue view section of the interface. (2) Mutation information. (3) User feedback buttons. (4) Mutation information download links. (5) Ancillary residue information panel.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256008&req=5

pcbi-1003951-g003: HIV Mutation Browser interface for Vpu residue 51 showing the navigation, protein and residue panels.(1) Options bar for the residue view section of the interface. (2) Mutation information. (3) User feedback buttons. (4) Mutation information download links. (5) Ancillary residue information panel.
Mentions: The web interface is organised in three panels: the navigation panel at the top; the protein panel in the middle; and the residue panel at the bottom (Figure 3).

Bottom Line: The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it.Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature.The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.

ABSTRACT
Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

Show MeSH