RSAT 2011: regulatory sequence analysis tools

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/.

Figure 1.

Flow chart of the Regulatory Sequence Analysis Tools (RSAT).

Figure 2.

Example of result from compare-matrices. Only the four best matches are displayed in the figure, the original Web page displayed five more matches. The second column displays a one-to-n alignment of matrix-logos. The next columns display multiple matching statistics, the corresponding ranks, and the mean rank. cor: Pearson’s correlation; Ncor: alignment width-normalized correlation; dEucl: Euclidian distance; NSW: width-normalized Sandelin–Wasserman similarity; rcor, rNcor, rdEucl, rNSW: ranks on the corresponding metrics; rank_mean: mean of these ranks; match_rank: rank of the alignments sorted by rank_mean.