ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data

Autores
Gonzalez, Sergio Alberto; Clavijo, Bernardo; Rivarola, Maximo Lisandro; Moreno, Patricio; Fernández, Paula; Dopazo, Joaquín; Paniego, Norma Beatriz
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. Conclusions: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net.
Inst. de Biotecnología
Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Clavijo, Bernardo. Norwich Research Park. Earlham Institute; Reino Unido
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Moreno, Patricio. Universidad de Buenos Aires. Facultad de Ingeniería. Instituto de Ingeniería Biomédica; Argentina
Fil: Fernández, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina
Fil: Dopazo, Joaquín Centro de Investigación Príncipe Felipe. Computational Genomics Department; España
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
BMC bioinformatics 18 (121) : 1-9. (2017)
Materia
Programas de ordenador
World Wide Web
Secuencia de ARN
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/502
Acceder
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network_name_str INTA Digital (INTA)
spelling ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic dataGonzalez, Sergio AlbertoClavijo, BernardoRivarola, Maximo LisandroMoreno, PatricioFernández, PaulaDopazo, JoaquínPaniego, Norma BeatrizProgramas de ordenadorWorld Wide WebSecuencia de ARNBackground: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. Conclusions: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net.Inst. de BiotecnologíaFil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Clavijo, Bernardo. Norwich Research Park. Earlham Institute; Reino UnidoFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Moreno, Patricio. Universidad de Buenos Aires. Facultad de Ingeniería. Instituto de Ingeniería Biomédica; ArgentinaFil: Fernández, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; ArgentinaFil: Dopazo, Joaquín Centro de Investigación Príncipe Felipe. Computational Genomics Department; EspañaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina2017-06-28T15:35:40Z2017-06-28T15:35:40Z2017-02-22info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/502https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2BMC bioinformatics 18 (121) : 1-9. (2017)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-11T10:22:04Zoai:localhost:20.500.12123/502instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-11 10:22:04.944INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
title ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
spellingShingle ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
Gonzalez, Sergio Alberto
Programas de ordenador
World Wide Web
Secuencia de ARN
title_short ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
title_full ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
title_fullStr ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
title_full_unstemmed ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
title_sort ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
dc.creator.none.fl_str_mv Gonzalez, Sergio Alberto
Clavijo, Bernardo
Rivarola, Maximo Lisandro
Moreno, Patricio
Fernández, Paula
Dopazo, Joaquín
Paniego, Norma Beatriz
author Gonzalez, Sergio Alberto
author_facet Gonzalez, Sergio Alberto
Clavijo, Bernardo
Rivarola, Maximo Lisandro
Moreno, Patricio
Fernández, Paula
Dopazo, Joaquín
Paniego, Norma Beatriz
author_role author
author2 Clavijo, Bernardo
Rivarola, Maximo Lisandro
Moreno, Patricio
Fernández, Paula
Dopazo, Joaquín
Paniego, Norma Beatriz
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Programas de ordenador
World Wide Web
Secuencia de ARN
topic Programas de ordenador
World Wide Web
Secuencia de ARN
dc.description.none.fl_txt_mv Background: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. Conclusions: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net.
Inst. de Biotecnología
Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Clavijo, Bernardo. Norwich Research Park. Earlham Institute; Reino Unido
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Moreno, Patricio. Universidad de Buenos Aires. Facultad de Ingeniería. Instituto de Ingeniería Biomédica; Argentina
Fil: Fernández, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina
Fil: Dopazo, Joaquín Centro de Investigación Príncipe Felipe. Computational Genomics Department; España
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Background: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. Results: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. Conclusions: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net.
publishDate 2017
dc.date.none.fl_str_mv 2017-06-28T15:35:40Z
2017-06-28T15:35:40Z
2017-02-22
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/502
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2
url http://hdl.handle.net/20.500.12123/502
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv BMC bioinformatics 18 (121) : 1-9. (2017)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.993085

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