Over-represented Transcription Factor Binding Site Prediction Tool (OTFBS)

(This is a mirror of the original OTFBS: http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS/)

Version: 1.0 (New! Release Data: Nov 8, 2004)

Summary:

• Genes of the same family or from the same tissue are usually regulated similarily. A nature assumption is that their promoters must contain a set of binding sites of a same set of Transcription Factors.
• OTFBS is a method base on TRANSFAC Matrix, it can detect over-represented motifs of known transcription factors from a set of related sequences. Particularly, promoters of a same gene family or from the same tissue can be submitted as a analysis subject. Promoters of putative co-regulated genes clustered with gene expression data should be also a good candidate to analysis. The version of TRANSFAC Matrix OTFBS currently uses is Release 6.0.

How to use OTFBS:

• Simply submit the upstream regulatory regions of a group of related genes, i.e. genes clustered together with microarray data, or just the genes of a same functional protein from a series of related species.
• Currently, the program only deals with the request with no more than 200 sequences.
• FAQ. (New! Maybe helpful if you get problems running OTFBS )
• OTFBS is described in detail in the paper: An approach to identify over-represented cis-elements in related sequences Nucl. Acids. Res. 2003 31: 1995-2005. You can also find it in the publication list.

You may want to submit your sequences to OTFBS for analysis here:

Contact: jiashun at genome dot ucsf dot edu

Last Modified: Mon. Nov 8 2004.