TY  - JOUR
A1  - Proost, Sebastian
A1  - Van Bel, Michiel
A1  - Vaneechoutte, Dries
A1  - Van de Peer, Yves
A1  - Inze, Dirk
A1  - Müller-Röber, Bernd
A1  - Vandepoele, Klaas
T1  - PLAZA 3.0: an access point for plant comparative genomics
JF  - Nucleic acids research
N2  - Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
Y1  - 2015
U6  - https://doi.org/10.1093/nar/gku986
SN  - 0305-1048
SN  - 1362-4962
VL  - 43
IS  - D1
SP  - D974
EP  - D981
PB  - Oxford Univ. Press
CY  - Oxford
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  - 
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  -