@article{ProostVanBelVaneechoutteetal.2015,
  author    = {Proost, Sebastian and Van Bel, Michiel and Vaneechoutte, Dries and Van de Peer, Yves and Inze, Dirk and M{\"u}ller-R{\"o}ber, Bernd and Vandepoele, Klaas},
  title     = {PLAZA 3.0: an access point for plant comparative genomics},
  series = {Nucleic acids research},
  volume    = {43},
  journal   = {Nucleic acids research},
  number    = {D1},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gku986},
  pages     = {D974 -- D981},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@misc{VanBelProostVanNesteetal.2013,
  author    = {Van Bel, Michiel and Proost, Sebastian and Van Neste, Christophe and Deforce, Dieter and Van de Peer, Yves and Vandepoele, Klaas},
  title     = {TRAPID},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {900},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43640},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436409},
  pages     = {12},
  year      = {2013},
  abstract  = {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/.},
  language  = {en}
}
@article{VanBelProostVanNesteetal.2013,
  author    = {Van Bel, Michiel and Proost, Sebastian and Van Neste, Christophe and Deforce, Dieter and Van de Peer, Yves and Vandepoele, Klaas},
  title     = {TRAPID - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes},
  series = {Genome biology : biology for the post-genomic era},
  volume    = {14},
  journal   = {Genome biology : biology for the post-genomic era},
  number    = {12},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1465-6906},
  doi       = {10.1186/gb-2013-14-12-r134},
  pages     = {10},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}