The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.
The discovery of regulatory motifs enriched in sets of DNA or RNA sequences is fundamental to the analysis of a great variety of functional genomics experiments. These motifs usually represent binding sites of proteins or non-coding RNAs, which are best described by position weight matrices (PWMs). We have recently developed XXmotif, a de novo motif discovery method that is able to directly optimize the statistical significance of PWMs. XXmotif can also score conservation and positional clustering of motifs. The XXmotif server provides (i) a list of significantly overrepresented motif PWMs with web logos and E-values; (ii) a graph with color-coded boxes indicating the positions of selected motifs in the input sequences; (iii) a histogram of the overall positional distribution for selected motifs and (iv) a page for each motif with all significant motif occurrences, their P-values for enrichment, conservation and localization, their sequence contexts and coordinates. Free access: http://xxmotif.genzentrum.lmu.de.
Gene Center, Department of Biochemistry, and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
Sebastian
S
Luehr
Holger
H
Hartmann
Johannes
J
Söding
D020407:Internet; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software