YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
Open Access
- 1 July 2003
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 31 (13) , 3586-3588
- https://doi.org/10.1093/nar/gkg618
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.Keywords
This publication has 6 references indexed in Scilit:
- Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosisMolecular Microbiology, 2003
- Discovery of novel transcription factor binding sites by statistical overrepresentationNucleic Acids Research, 2002
- Separating real motifs from their artifactsBioinformatics, 2001
- Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.Bioinformatics, 1999
- Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitationNature Biotechnology, 1998
- Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple AlignmentScience, 1993