@article {432, title = {ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.}, journal = {BMC Bioinformatics}, volume = {18}, year = {2017}, month = {2017 Feb 22}, pages = {121}, 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 .

}, keywords = {Animals, Databases, Genetic, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Internet, Sequence Analysis, RNA, Transcriptome, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/s12859-017-1494-2}, author = {Gonzalez, Sergio and Clavijo, Bernardo and Rivarola, M{\'a}ximo and Moreno, Patricio and Fernandez, Paula and Dopazo, Joaquin and Paniego, Norma} }