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  RSAT 2011: regulatory sequence analysis tools

Thomas-Chollier, M., Defrance, M., Medina-Rivera, A., Sand, O., Herrmann, C., Thieffry, D., et al. (2011). RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res, 39(Web Server issue), W86-91. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21715389 http://nar.oxfordjournals.org/content/39/suppl_2/W86.full.pdf.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-792A-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-792B-A
Genre: Journal Article

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Thomas-Chollier, M.1, Author              
Defrance, M., Author
Medina-Rivera, A., Author
Sand, O., Author
Herrmann, C., Author
Thieffry, D., Author
van Helden, J., Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

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Free keywords: Binding Sites; Genomics; Regulatory Elements, Transcriptional; *Regulatory Sequences, Nucleic Acid; *Software; Transcription Factors/metabolism
 Abstract: 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/.

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 Dates: 2011
 Publication Status: Published in print
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Title: Nucleic Acids Res
Source Genre: Journal
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Pages: - Volume / Issue: 39 (Web Server issue) Sequence Number: - Start / End Page: W86 - 91 Identifier: ISSN: 1362-4962 (Electronic) 0305-1048 (Linking)