TY  - JOUR
A1  - Van Bel, Michiel
A1  - Proost, Sebastian
A1  - Van Neste, Christophe
A1  - Deforce, Dieter
A1  - Van de Peer, Yves
A1  - Vandepoele, Klaas
T1  - TRAPID - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
JF  - Genome biology : biology for the post-genomic era
N2  - 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.
Y1  - 2013
U6  - https://doi.org/10.1186/gb-2013-14-12-r134
SN  - 1465-6906
SN  - 1474-760X
VL  - 14
IS  - 12
PB  - BioMed Central
CY  - London
ER  - 
TY  - GEN
A1  - Van Bel, Michiel
A1  - Proost, Sebastian
A1  - Van  Neste, Christophe
A1  - Deforce, Dieter
A1  - Van de Peer, Yves
A1  - Vandepoele, Klaas
T1  - TRAPID
BT  - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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/.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 900 
KW  - gene ontology
KW  - gene family
KW  - functional annotation
KW  - reference database
KW  - reference proteomes
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436409
SN  - 1866-8372
IS  - 900
ER  -