Difference between revisions of "RSAT peak-motifs"
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|input format=A fasta file containing the peaks (optionally a second one for differential analysis) | |input format=A fasta file containing the peaks (optionally a second one for differential analysis) | ||
|output format=HTML, text, graphics (png) | |output format=HTML, text, graphics (png) | ||
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|language=workflow in Perl, Web interface in CGI, motif analysis algorithms in Perl + python + C | |language=workflow in Perl, Web interface in CGI, motif analysis algorithms in Perl + python + C | ||
|library=None required for the Web interface. Auto installation script for the stand-alone version of RSAT. | |library=None required for the Web interface. Auto installation script for the stand-alone version of RSAT. | ||
Revision as of 07:14, 15 October 2011
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Application data |
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| Created by | Jacques van Heldencit, Morgane Thomas-Chollierc, Matthieu Defrance, Olivier Sand, Denis Thieffry and Carl Herrmann |
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| Biological application domain(s) | ChIP-seq
regulatory genomics epigenomicsProperty "Biological domain" (as page type) with input value "ChIP-seq regulatory genomics epigenomics" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. |
| Principal bioinformatics method(s) | motif discovery
motif scanning motif comparisonProperty "Bioinformatics method" (as page type) with input value "motif discovery motif scanning motif comparison" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. |
| Technology | any |
| Created at | Université Libre de Bruxelles (Brussels, Belgium)
Université de la Méditerrannée (Marseille, France) Max Planck Institute for Molecular Genetics (Berlin, Germany) Pasteur (Lille, France) IBENS (Paris, France) |
| Maintained? | Yes |
| Input format(s) | A fasta file containing the peaks (optionally a second one for differential analysis) |
| Output format(s) | HTML, text, graphics (png) |
| Programming language(s) | workflow in Perl, Web interface in CGI, motif analysis algorithms in Perl + python + C |
| Software libraries | None required for the Web interface. Auto installation script for the stand-alone version of RSAT. |
| Licence | freeware license for non-commercial and non-military utilization |
| Operating system(s) | Web form + Web services (SOAP/WSDL) + stand-alone (Unix, Mac OSX, Linux). |
Summary: A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies.
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Description
The peak-motif workflow is integrated in the software suite "Regulatory Sequence Analysis Tools" (RSAT). It combines:
- analysis of sequence composition (peak lengths, global and positional distribution of nucleotide and dinucleotide frequencies);
- motif discovery, based on complementary criteria: global over-representation of words (oligo-analysis) and spaced pairs (dyad-analysis), heterogeneity in word positional distributions (position-analysis), detection of local enrichment of words in positional windows of centered peaks (local-words);
- motif comparison: discovered motifs are compared with databases of known motifs (JASPAR, RegulonDB) or with user-supplied motifs;
- binding site prediction: matching of the discovered motifs against peak sequences;
- visualization: predicted sites in bed format, suitable for the UCSC genome browser;
Links
References
To add a reference for RSAT peak-motifs, enter the PubMed ID in the field below and click 'Add'.
Search for "RSAT peak-motifs" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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