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

  • 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.

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Metadaten
Author:Michiel Van Bel, Sebastian Proost, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, Klaas Vandepoele
DOI:https://doi.org/10.1186/gb-2013-14-12-r134
ISSN:1465-6906 (print)
ISSN:1474-760X (online)
Parent Title (English):Genome biology : biology for the post-genomic era
Publisher:BioMed Central
Place of publication:London
Document Type:Article
Language:English
Year of first Publication:2013
Year of Completion:2013
Release Date:2017/03/26
Volume:14
Issue:12
Pagenumber:10
Funder:Ghent University [01MR0310W]
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Chemie
Peer Review:Referiert