期刊
NUCLEIC ACIDS RESEARCH
卷 40, 期 W1, 页码 W104-W109出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks602
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资金
- Deutsche Forschungsgemeinschaft (DFG) [SFB646]
- Center for Protein Science Munich (CIPSM)
- Ludwig-Maximilians-Universitat Munchen
- Excellence Initiative of the German Bundesministerium fur Bildung und Forschung
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.
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