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/.
Author details: | Michiel Van BelORCiD, Sebastian ProostORCiD, Christophe Van NesteORCiD, Dieter Deforce, Yves Van de PeerORCiD, Klaas VandepoeleORCiD |
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URN: | urn:nbn:de:kobv:517-opus4-436409 |
DOI: | https://doi.org/10.25932/publishup-43640 |
ISSN: | 1866-8372 |
Title of parent work (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 |
Publication series (Volume number): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (900) |
Publication type: | Postprint |
Language: | English |
Date of first publication: | 2020/05/19 |
Publication year: | 2013 |
Publishing institution: | Universität Potsdam |
Release date: | 2020/05/19 |
Tag: | functional annotation; gene family; gene ontology; reference database; reference proteomes |
Issue: | 900 |
Number of pages: | 12 |
Source: | Genome Biology 14 (2013) R134 DOI: 10.1186/gb-2013-14-12-r134 |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät |
DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
Peer review: | Referiert |
Publishing method: | Open Access |
License (English): | Creative Commons - Namensnennung 2.0 Generic |
External remark: | Bibliographieeintrag der Originalveröffentlichung/Quelle |