02375nas a2200313 4500008004100000022001400041245011300055210006900168260001600237300000800253490000700261520133500268653001201603653002301615653003001638653004201668653001301710653002701723653001801750653002801768100002101796700002201817700002201839700002101861700002101882700002001903700001901923856011901942 2017 eng d a1471-210500aATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.0 aATGC transcriptomics a webbased application to integrate explore c2017 Feb 22 a1210 v183 a
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 .
10aAnimals10aDatabases, Genetic10aGene Expression Profiling10aHigh-Throughput Nucleotide Sequencing10aInternet10aSequence Analysis, RNA10aTranscriptome10aUser-Computer Interface1 aGonzalez, Sergio1 aClavijo, Bernardo1 aRivarola, Máximo1 aMoreno, Patricio1 aFernandez, Paula1 aDopazo, Joaquin1 aPaniego, Norma uhttp://clinbioinfosspa.es/content/atgc-transcriptomics-web-based-application-integrate-explore-and-analyze-de-novo