TRAPID

  • 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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Metadaten
Author:Michiel Van BelORCiD, Sebastian ProostORCiD, Christophe Van NesteORCiD, Dieter Deforce, Yves Van de PeerORCiD, Klaas VandepoeleORCiD
URN:urn:nbn:de:kobv:517-opus4-436409
DOI:https://doi.org/10.25932/publishup-43640
ISSN:1474-760X
Parent Title (German):Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
Subtitle (English):an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
Series (Serial Number):Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (900)
Document Type:Postprint
Language:English
Date of first Publication:2020/05/19
Year of Completion:2013
Publishing Institution:Universität Potsdam
Release Date:2020/05/19
Tag:functional annotation; gene family; gene ontology; reference database; reference proteomes
Issue:900
Pagenumber:12
Source:Genome Biology 14 (2013) R134 DOI: 10.1186/gb-2013-14-12-r134
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Peer Review:Referiert
Publication Way:Open Access
Licence (English):License LogoCreative Commons - Namensnennung 2.0 Generic
Notes extern:Bibliographieeintrag der Originalveröffentlichung/Quelle