An automated genotyping system for analysis of HIV-1 and other microbial sequences
Identifieur interne : 001820 ( Main/Exploration ); précédent : 001819; suivant : 001821An automated genotyping system for analysis of HIV-1 and other microbial sequences
Auteurs : Tulio De Oliveira [Royaume-Uni] ; Koen Deforche [Belgique] ; Sharon Cassol [Afrique du Sud] ; Mika Salminen [Finlande] ; Dimitris Paraskevis [Belgique] ; Chris Seebregts [Afrique du Sud] ; Joe Snoeck [Belgique] ; Estrelita Janse Van Rensburg [Afrique du Sud] ; Annemarie M. J. Wensing [Pays-Bas] ; David A. Van De Vijver [Pays-Bas] ; Charles A. Boucher [Pays-Bas] ; Ricardo Camacho [Portugal] ; Anne-Mieke Vandamme [Belgique]Source :
- Bioinformatics [ 1367-4803 ] ; 2005-01.
Abstract
Motivation: Genetic analysis of HIV-1 is important not only for vaccine development, but also to guide treatment strategies, track the emergence of new viral variants and ensure that diagnostic assays are contemporary and fully optimized. However, most genotyping methods are laborious and complex, and involve the use of multiple software applications. Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens. Results: The new REGA subtyping tool, developed using Java programming and PERL scripts, combines phylogenetic analyses with bootscanning methods for the genetic subtyping of full-length and subgenomic fragments of HIV-1. When used to investigate the subtype of previously published reference datasets that were analysed using manual phylogenetic methods, the automated method correctly identified 97.5–100% of non-recombinant and circulating recombinant forms of HIV-1, including 108 full-length, 108 gag and 221 env sequences downloaded from the Los Alamos database. Availability: The tool, which can be easily downloaded and installed on either a UNIX or Linux-based computer system, is available at http://www.bioafrica.net/subtypetool/html/ Contact: tulio.deoliveira@zoology.oxford.ac.uk
Url:
DOI: 10.1093/bioinformatics/bti607
Affiliations:
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Boucher</name><affiliation wicri:level="1"><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Medical Microbiology, Sub department of Virology and Eijkman Winkler Institute, University Medical Center Utrecht Utrecht</wicri:regionArea><wicri:noRegion>University Medical Center Utrecht Utrecht</wicri:noRegion></affiliation></author><author><name sortKey="Camacho, Ricardo" sort="Camacho, Ricardo" uniqKey="Camacho R" first="Ricardo" last="Camacho">Ricardo Camacho</name><affiliation wicri:level="1"><country xml:lang="fr">Portugal</country><wicri:regionArea>Virology Laboratory, Hospital Egas Moniz Lisbon</wicri:regionArea><wicri:noRegion>Hospital Egas Moniz Lisbon</wicri:noRegion></affiliation></author><author><name sortKey="Vandamme, Anne Mieke" sort="Vandamme, Anne Mieke" uniqKey="Vandamme A" first="Anne-Mieke" last="Vandamme">Anne-Mieke Vandamme</name><affiliation wicri:level="1"><country xml:lang="fr">Belgique</country><wicri:regionArea>Rega Institute for Medical Research, Katholieke Universiteit Leuven Leuven</wicri:regionArea><wicri:noRegion>Katholieke Universiteit Leuven Leuven</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2005-01">2005-01</date><biblScope unit="volume">21</biblScope><biblScope unit="issue">19</biblScope><biblScope unit="page" from="3797">3797</biblScope><biblScope unit="page" to="3800">3800</biblScope></imprint><idno type="ISSN">1367-4803</idno></series><idno type="istex">CAFE94CD146C4A5999DFFCB53FF376A7296C5FB8</idno><idno type="DOI">10.1093/bioinformatics/bti607</idno><idno type="local">bti607</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: Genetic analysis of HIV-1 is important not only for vaccine development, but also to guide treatment strategies, track the emergence of new viral variants and ensure that diagnostic assays are contemporary and fully optimized. However, most genotyping methods are laborious and complex, and involve the use of multiple software applications. Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens. Results: The new REGA subtyping tool, developed using Java programming and PERL scripts, combines phylogenetic analyses with bootscanning methods for the genetic subtyping of full-length and subgenomic fragments of HIV-1. When used to investigate the subtype of previously published reference datasets that were analysed using manual phylogenetic methods, the automated method correctly identified 97.5–100% of non-recombinant and circulating recombinant forms of HIV-1, including 108 full-length, 108 gag and 221 env sequences downloaded from the Los Alamos database. Availability: The tool, which can be easily downloaded and installed on either a UNIX or Linux-based computer system, is available at http://www.bioafrica.net/subtypetool/html/ Contact: tulio.deoliveira@zoology.oxford.ac.uk</div></front></TEI><affiliations><list><country><li>Afrique du Sud</li><li>Belgique</li><li>Finlande</li><li>Pays-Bas</li><li>Portugal</li><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="De Oliveira, Tulio" sort="De Oliveira, Tulio" uniqKey="De Oliveira T" first="Tulio" last="De Oliveira">Tulio De Oliveira</name></noRegion></country><country name="Belgique"><noRegion><name sortKey="Deforche, Koen" sort="Deforche, Koen" uniqKey="Deforche K" first="Koen" last="Deforche">Koen Deforche</name></noRegion><name sortKey="Paraskevis, Dimitris" sort="Paraskevis, Dimitris" uniqKey="Paraskevis D" first="Dimitris" last="Paraskevis">Dimitris Paraskevis</name><name sortKey="Snoeck, Joe" sort="Snoeck, Joe" uniqKey="Snoeck J" first="Joe" last="Snoeck">Joe Snoeck</name><name sortKey="Vandamme, Anne Mieke" sort="Vandamme, Anne Mieke" uniqKey="Vandamme A" first="Anne-Mieke" last="Vandamme">Anne-Mieke Vandamme</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Cassol, Sharon" sort="Cassol, Sharon" uniqKey="Cassol S" first="Sharon" last="Cassol">Sharon Cassol</name></noRegion><name sortKey="Seebregts, Chris" sort="Seebregts, Chris" uniqKey="Seebregts C" first="Chris" last="Seebregts">Chris Seebregts</name><name sortKey="Van Rensburg, Estrelita Janse" sort="Van Rensburg, Estrelita Janse" uniqKey="Van Rensburg E" first="Estrelita Janse" last="Van Rensburg">Estrelita Janse Van Rensburg</name></country><country name="Finlande"><noRegion><name sortKey="Salminen, Mika" sort="Salminen, Mika" uniqKey="Salminen M" first="Mika" last="Salminen">Mika Salminen</name></noRegion></country><country name="Pays-Bas"><noRegion><name sortKey="Wensing, Annemarie M J" sort="Wensing, Annemarie M J" uniqKey="Wensing A" first="Annemarie M. J." last="Wensing">Annemarie M. J. Wensing</name></noRegion><name sortKey="Boucher, Charles A" sort="Boucher, Charles A" uniqKey="Boucher C" first="Charles A." last="Boucher">Charles A. Boucher</name><name sortKey="Van De Vijver, David A" sort="Van De Vijver, David A" uniqKey="Van De Vijver D" first="David A." last="Van De Vijver">David A. Van De Vijver</name><name sortKey="Wensing, Annemarie M J" sort="Wensing, Annemarie M J" uniqKey="Wensing A" first="Annemarie M. J." last="Wensing">Annemarie M. J. Wensing</name></country><country name="Portugal"><noRegion><name sortKey="Camacho, Ricardo" sort="Camacho, Ricardo" uniqKey="Camacho R" first="Ricardo" last="Camacho">Ricardo Camacho</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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