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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.
Author details: | Michiel Van Bel, Sebastian ProostORCiD, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, Klaas Vandepoele |
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DOI: | https://doi.org/10.1186/gb-2013-14-12-r134 |
ISSN: | 1465-6906 |
ISSN: | 1474-760X |
Title of parent work (English): | Genome biology : biology for the post-genomic era |
Publisher: | BioMed Central |
Place of publishing: | London |
Publication type: | Article |
Language: | English |
Year of first publication: | 2013 |
Publication year: | 2013 |
Release date: | 2017/03/26 |
Volume: | 14 |
Issue: | 12 |
Number of pages: | 10 |
Funding institution: | Ghent University [01MR0310W] |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Chemie |
Peer review: | Referiert |
External remark: | Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 900 |