The XXmotif web server for eXhaustive, weight matriX-based motif discovery in 
nucleotide sequences.

Luehr, S.; Hartmann, H.; Söding, J.

doi:10.1093/nar/gks602

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The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.

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Söding, J.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

Luehr, S., Hartmann, H., & Söding, J. (2012). The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. Nucleic Acids Research, 40(W1), W104-W109. doi:10.1093/nar/gks602.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0015-8D2D-A

Abstract

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.