The XXmotif web server can discover motifs that are enriched in sets of nucleotide sequences provided by the user. XXmotif uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.
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Nucleic Acids Res. 2012 Jul;40(Web Server issue):W104-9. doi: 10.1093/nar/gks602. Epub 2012 Jun 12.
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.
Luehr S, Hartmann H, Söding J.