RSAT 2011: regulatory sequence analysis tools

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMB...

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Bibliographic Details
Published in:Nucleic acids research 2011-07, Vol.39 (suppl_2), p.W86-W91
Main Authors: Thomas-Chollier, Morgane, Defrance, Matthieu, Medina-Rivera, Alejandra, Sand, Olivier, Herrmann, Carl, Thieffry, Denis, van Helden, Jacques
Format: Article
Language:English
Subjects:
Binding Sites
Bioinformatics
Computer Science
Genomics
Life Sciences
Regulatory Elements, Transcriptional
Regulatory Sequences, Nucleic Acid
Software
Transcription Factors - metabolism
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Summary:RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkr377