A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2009 |
| Outros Autores: | , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/1900 |
Resumo: | Oswaldo Cruz Foundation. Laboratório Avançado de Saúde Pública. Centro de Pesquisas Gonçalo Moniz. BA, Brazil. |
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Alcantara, Luiz Carlos JúniorCassol, SharonLibin, PieterDeforche, KoenPybus, Oliver G.Van Ranst, MarcCastro Filho, Bernardo GalvãoVandamme, Anne-MiekeOliveira, Tulio de2011-04-13T04:16:28Z2011-04-13T04:16:28Z2009ALCÂNTARA JUNIOR, L. C. et al. A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Research, v.37, n. Web Server issue, p. W634-42, 2009.0305-1048https://www.arca.fiocruz.br/handle/icict/190010.1093/nar/gkp455engA Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequencesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleOswaldo Cruz Foundation. Laboratório Avançado de Saúde Pública. Centro de Pesquisas Gonçalo Moniz. BA, Brazil.MRC Unit for Inflammation and Immunity, Department of Immunology, University of Pretoria and Tshwane Academic Division of the National Health Laboratory Service, Pretoria, South Africa.Laboratory for Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Belgica.MyBioData bvba, Rotselaar, Belgica.Department of Zoology, University of Oxford, UK.Laboratory for Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Belgica.Oswaldo Cruz Foundation. Laboratório Avançado de Saúde Pública. Centro de Pesquisas Gonçalo Moniz. BA, Brazil.Laboratory for Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Belgica.Africa Centre for Health and Population Studies, University of KwaZulu-Natal, South Africa.Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/, http://lasp.cpqgm.fiocruz.br/virus-genotype/html/, http://jose.med.kuleuven.be/genotypetool/html/.Variação GenéticaHIV-1Vírus da Hepatite BHepacivirusSoftwareVírusAnálise de SequênciaRecombinação Genéticainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALA standardized framework for accurate,.pdfA standardized framework for accurate,.pdfapplication/pdf3875332https://www.arca.fiocruz.br/bitstream/icict/1900/1/A%20standardized%20framework%20for%20accurate%2c.pdfeb44a684d67b6c4e84b4482668d6a213MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81648https://www.arca.fiocruz.br/bitstream/icict/1900/2/license.txte095249ac7cacefbfe39684dfe45e706MD52TEXTA standardized framework for accurate,.pdf.txtA standardized framework for accurate,.pdf.txtExtracted texttext/plain40349https://www.arca.fiocruz.br/bitstream/icict/1900/5/A%20standardized%20framework%20for%20accurate%2c.pdf.txt7b0c5adf66aa54a83c4ef17844ba989eMD55THUMBNAILA standardized framework for accurate,.pdf.jpgA standardized framework for accurate,.pdf.jpgGenerated Thumbnailimage/jpeg2557https://www.arca.fiocruz.br/bitstream/icict/1900/4/A%20standardized%20framework%20for%20accurate%2c.pdf.jpg2f4c615b8b34278c8db2cf04b341e9ddMD54icict/19002023-03-15 14:33:56.783oai:www.arca.fiocruz.br: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Repositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-03-15T17:33:56Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.pt_BR.fl_str_mv |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| title |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| spellingShingle |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences Alcantara, Luiz Carlos Júnior Variação Genética HIV-1 Vírus da Hepatite B Hepacivirus Software Vírus Análise de Sequência Recombinação Genética |
| title_short |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| title_full |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| title_fullStr |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| title_full_unstemmed |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| title_sort |
A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences |
| author |
Alcantara, Luiz Carlos Júnior |
| author_facet |
Alcantara, Luiz Carlos Júnior Cassol, Sharon Libin, Pieter Deforche, Koen Pybus, Oliver G. Van Ranst, Marc Castro Filho, Bernardo Galvão Vandamme, Anne-Mieke Oliveira, Tulio de |
| author_role |
author |
| author2 |
Cassol, Sharon Libin, Pieter Deforche, Koen Pybus, Oliver G. Van Ranst, Marc Castro Filho, Bernardo Galvão Vandamme, Anne-Mieke Oliveira, Tulio de |
| author2_role |
author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Alcantara, Luiz Carlos Júnior Cassol, Sharon Libin, Pieter Deforche, Koen Pybus, Oliver G. Van Ranst, Marc Castro Filho, Bernardo Galvão Vandamme, Anne-Mieke Oliveira, Tulio de |
| dc.subject.decs.pt_BR.fl_str_mv |
Variação Genética HIV-1 Vírus da Hepatite B Hepacivirus Software Vírus Análise de Sequência Recombinação Genética |
| topic |
Variação Genética HIV-1 Vírus da Hepatite B Hepacivirus Software Vírus Análise de Sequência Recombinação Genética |
| description |
Oswaldo Cruz Foundation. Laboratório Avançado de Saúde Pública. Centro de Pesquisas Gonçalo Moniz. BA, Brazil. |
| publishDate |
2009 |
| dc.date.issued.fl_str_mv |
2009 |
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2011-04-13T04:16:28Z |
| dc.date.available.fl_str_mv |
2011-04-13T04:16:28Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
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ALCÂNTARA JUNIOR, L. C. et al. A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Research, v.37, n. Web Server issue, p. W634-42, 2009. |
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https://www.arca.fiocruz.br/handle/icict/1900 |
| dc.identifier.issn.none.fl_str_mv |
0305-1048 |
| dc.identifier.doi.none.fl_str_mv |
10.1093/nar/gkp455 |
| identifier_str_mv |
ALCÂNTARA JUNIOR, L. C. et al. A Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Research, v.37, n. Web Server issue, p. W634-42, 2009. 0305-1048 10.1093/nar/gkp455 |
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