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

TitleATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.
Publication TypeJournal Article
Year of Publication2017
AuthorsGonzalez, S, Clavijo, B, Rivarola, M, Moreno, P, Fernandez, P, Dopazo, J, Paniego, N
JournalBMC Bioinformatics
Volume18
Issue1
Pagination121
Date Published2017 Feb 22
ISSN1471-2105
KeywordsAnimals; Databases, Genetic; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Internet; Sequence Analysis, RNA; Transcriptome; User-Computer Interface
Abstract

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 .

DOI10.1186/s12859-017-1494-2
Alternate JournalBMC Bioinformatics
PubMed ID28222698
PubMed Central IDPMC5320735