ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data
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 evaluat...
| Main Authors: | , , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.12123/502 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2 |
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| author | Gonzalez, Sergio Alberto Clavijo, Bernardo Rivarola, Maximo Lisandro Moreno, Patricio Fernández, Paula Dopazo, Joaquín Paniego, Norma Beatriz |
| author_browse | Clavijo, Bernardo Dopazo, Joaquín Fernández, Paula Gonzalez, Sergio Alberto Moreno, Patricio Paniego, Norma Beatriz Rivarola, Maximo Lisandro |
| author_facet | Gonzalez, Sergio Alberto Clavijo, Bernardo Rivarola, Maximo Lisandro Moreno, Patricio Fernández, Paula Dopazo, Joaquín Paniego, Norma Beatriz |
| author_sort | Gonzalez, Sergio Alberto |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA502 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA5022017-12-22T16:45:00Z ATGC transcriptomics : a web-based application to integrate, explore and analyze de novo transcriptomic data Gonzalez, Sergio Alberto Clavijo, Bernardo Rivarola, Maximo Lisandro Moreno, Patricio Fernández, Paula Dopazo, Joaquín Paniego, Norma Beatriz Programas de ordenador World Wide Web Secuencia de ARN 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 2017-06-28T15:35:40Z 2017-06-28T15:35:40Z 2017-02-22 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/502 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2 eng 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) application/pdf BMC bioinformatics 18 (121) : 1-9. (2017) |
| spellingShingle | Programas de ordenador World Wide Web Secuencia de ARN Gonzalez, Sergio Alberto Clavijo, Bernardo Rivarola, Maximo Lisandro Moreno, Patricio Fernández, Paula Dopazo, Joaquín Paniego, Norma Beatriz 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 |
| 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_short | 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 |
| topic | Programas de ordenador World Wide Web Secuencia de ARN |
| url | http://hdl.handle.net/20.500.12123/502 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1494-2 |
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