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TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

(2013) GENOME BIOLOGY. 14(12).
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
PLAZA, MODEL, DATABASE, PLATFORM, PERFORMANCE, ANNOTATION, MULTIPLE SEQUENCE ALIGNMENT, COMPARATIVE GENOMICS, GENE, SEARCH TOOL

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Citation

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Chicago
Van Bel, Michiel, Sebastian Proost, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, and Klaas Vandepoele. 2013. “TRAPID : an Efficient Online Tool for the Functional and Comparative Analysis of De Novo RNA-Seq Transcriptomes.” Genome Biology 14 (12).
APA
Van Bel, M., Proost, S., Van Neste, C., Deforce, D., Van de Peer, Y., & Vandepoele, K. (2013). TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. GENOME BIOLOGY, 14(12).
Vancouver
1.
Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K. TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. GENOME BIOLOGY. 2013;14(12).
MLA
Van Bel, Michiel, Sebastian Proost, Christophe Van Neste, et al. “TRAPID : an Efficient Online Tool for the Functional and Comparative Analysis of De Novo RNA-Seq Transcriptomes.” GENOME BIOLOGY 14.12 (2013): n. pag. Print.
@article{4349395,
  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.},
  articleno    = {R134},
  author       = {Van Bel, Michiel and Proost, Sebastian and Van Neste, Christophe and Deforce, Dieter and Van de Peer, Yves and Vandepoele, Klaas},
  issn         = {1465-6906},
  journal      = {GENOME BIOLOGY},
  keyword      = {PLAZA,MODEL,DATABASE,PLATFORM,PERFORMANCE,ANNOTATION,MULTIPLE SEQUENCE ALIGNMENT,COMPARATIVE GENOMICS,GENE,SEARCH TOOL},
  language     = {eng},
  number       = {12},
  pages        = {10},
  title        = {TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes},
  url          = {http://dx.doi.org/10.1186/gb-2013-14-12-r134},
  volume       = {14},
  year         = {2013},
}

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