HCVIVdb: The hepatitis-C IRES variation database

Background: Sequence variability in the hepatitis C virus (HCV) genome has led to the development and classification of six genotypes and a number of subtypes. The HCV 5′ untranslated region mainly comprises an internal ribosomal entry site (IRES) responsible for cap-independent synthesis of the vir...

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Autores: Floden, Evan Wade, Khawaja, Anas, Vopálenský, Václav, Pospíšek, Martin
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/27877
Acceso en línea:http://hdl.handle.net/10230/27877
http://dx.doi.org/10.1186/s12866-016-0804-6
Access Level:acceso abierto
Palabra clave:Hepatitis C
HCV
Internal ribosome entry site
IRES
Translation efficiency
Database
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spelling HCVIVdb: The hepatitis-C IRES variation databaseFloden, Evan WadeKhawaja, AnasVopálenský, VáclavPospíšek, MartinHepatitis CHCVInternal ribosome entry siteIRESTranslation efficiencyDatabaseBackground: Sequence variability in the hepatitis C virus (HCV) genome has led to the development and classification of six genotypes and a number of subtypes. The HCV 5′ untranslated region mainly comprises an internal ribosomal entry site (IRES) responsible for cap-independent synthesis of the viral polyprotein and is conserved among all HCV genotypes. Description: Considering the possible high impact of variations in HCV IRES on viral protein production and thus virus replication, we decided to collect the available data on known nucleotide variants in the HCV IRES and their impact on IRES function in translation initiation. The HCV IRES variation database (HCVIVdb) is a collection of naturally occurring and engineered mutation entries for the HCV IRES. Each entry contains contextual information pertaining to the entry such as the HCV genotypic background and links to the original publication. Where available, quantitative data on the IRES efficiency in translation have been collated along with details on the reporter system used to generate the data. Data are displayed both in a tabular and graphical formats and allow direct comparison of results from different experiments. Together the data provide a central resource for researchers in the IRES and hepatitis C-oriented fields. Conclusion: The collation of over 1900 mutations enables systematic analysis of the HCV IRES. The database is mainly dedicated to detailed comparative and functional analysis of all the HCV IRES domains, which can further lead to the development of site-specific drug designs and provide a guide for future experiments. HCVIVdb is available at http://www.hcvivdb.org.BioMed Central201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/27877http://dx.doi.org/10.1186/s12866-016-0804-6reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBMC Microbiology. 2016;16:187© 2016 The Author(s). Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/278772026-06-12T07:21:37Z
dc.title.none.fl_str_mv HCVIVdb: The hepatitis-C IRES variation database
title HCVIVdb: The hepatitis-C IRES variation database
spellingShingle HCVIVdb: The hepatitis-C IRES variation database
Floden, Evan Wade
Hepatitis C
HCV
Internal ribosome entry site
IRES
Translation efficiency
Database
title_short HCVIVdb: The hepatitis-C IRES variation database
title_full HCVIVdb: The hepatitis-C IRES variation database
title_fullStr HCVIVdb: The hepatitis-C IRES variation database
title_full_unstemmed HCVIVdb: The hepatitis-C IRES variation database
title_sort HCVIVdb: The hepatitis-C IRES variation database
dc.creator.none.fl_str_mv Floden, Evan Wade
Khawaja, Anas
Vopálenský, Václav
Pospíšek, Martin
author Floden, Evan Wade
author_facet Floden, Evan Wade
Khawaja, Anas
Vopálenský, Václav
Pospíšek, Martin
author_role author
author2 Khawaja, Anas
Vopálenský, Václav
Pospíšek, Martin
author2_role author
author
author
dc.subject.none.fl_str_mv Hepatitis C
HCV
Internal ribosome entry site
IRES
Translation efficiency
Database
topic Hepatitis C
HCV
Internal ribosome entry site
IRES
Translation efficiency
Database
description Background: Sequence variability in the hepatitis C virus (HCV) genome has led to the development and classification of six genotypes and a number of subtypes. The HCV 5′ untranslated region mainly comprises an internal ribosomal entry site (IRES) responsible for cap-independent synthesis of the viral polyprotein and is conserved among all HCV genotypes. Description: Considering the possible high impact of variations in HCV IRES on viral protein production and thus virus replication, we decided to collect the available data on known nucleotide variants in the HCV IRES and their impact on IRES function in translation initiation. The HCV IRES variation database (HCVIVdb) is a collection of naturally occurring and engineered mutation entries for the HCV IRES. Each entry contains contextual information pertaining to the entry such as the HCV genotypic background and links to the original publication. Where available, quantitative data on the IRES efficiency in translation have been collated along with details on the reporter system used to generate the data. Data are displayed both in a tabular and graphical formats and allow direct comparison of results from different experiments. Together the data provide a central resource for researchers in the IRES and hepatitis C-oriented fields. Conclusion: The collation of over 1900 mutations enables systematic analysis of the HCV IRES. The database is mainly dedicated to detailed comparative and functional analysis of all the HCV IRES domains, which can further lead to the development of site-specific drug designs and provide a guide for future experiments. HCVIVdb is available at http://www.hcvivdb.org.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/27877
http://dx.doi.org/10.1186/s12866-016-0804-6
url http://hdl.handle.net/10230/27877
http://dx.doi.org/10.1186/s12866-016-0804-6
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv BMC Microbiology. 2016;16:187
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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