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

GONZALEZ S; MORENO P; PANIEGO NORMA; RIVAROLA M; DOPAZO JOAQUIN; CLAVIJO BJ; FERNANDEZ P; GONZALEZ S; MORENO P; PANIEGO NORMA; RIVAROLA M; DOPAZO JOAQUIN; CLAVIJO BJ; FERNANDEZ P

BMC BIOINFORMATICS

BIOMED CENTRAL LTD

Lugar: Londres; Año: 2017 vol. 18 p. 121 - 130

1471-2105

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 data 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 for non-commercial use at http://atgcinta.sourceforge.net.