TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Genome Biology
Michiel Van BelKlaas Vandepoele

Abstract

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.

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Citations

Jan 23, 2016·Molecular Breeding : New Strategies in Plant Improvement·Claire Lessa Alvim KameiLuisa M Trindade
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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

FrameDP
RAPSearch2
MySQL
KEGG Orthology
BLASTX
Archaeopteryx
Blast2GO
TIGR
SOAPdenovo
DB

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