title: YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation.
abstract: A fundamental challenge facing biologists is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated. The program YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores. This note describes the YMF web software, available at http://bio.cs.washington.edu/software.html.
authors.affiliation: Center for Studies in Physics and Biology, Box 25, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
authors.forename: Martin
authors.initials: M
authors.lastname: Tompa
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003627:Data Interpretation, Statistical; D020407:Internet; D009169:Mycobacterium tuberculosis / Q000235:genetics; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors