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

Michiel Van Bel12, Sebastian Proost34, Christophe Van Neste5, Dieter Deforce5, Yves Van de Peer126 and Klaas Vandepoele12*

Author Affiliations

1 Department of Plant Systems Biology, VIB-Universiteit Gent, Technologiepark 927, B-9052 Gent, Belgium

2 Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium

3 University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straβe 24-25, Haus 20, 14476 Potsdam-Golm, Germany

4 Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany

5 Department of Pharmaceutics, Ghent University, B-9052 Gent, Belgium

6 Department of Genetics, Genome Research Institute, University of Pretoria, Pretoria, South Africa

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Genome Biology 2013, 14:R134  doi:10.1186/gb-2013-14-12-r134

Published: 13 December 2013

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/ webcite.