Title

A web server for transcription factor binding site prediction

Authors

Gang Su, Binchen Mao, Jin Wang

Affiliation

The State Key Laboratory of Pharmaceutical Biotechnology and Model Animal Research Center, School of Life Science, Nanjing University, Nanjing 210093, China.

E-mail*

jwang@nju.edu.cn; * Corresponding author

Article Type

Web Server

Date

received April 30, 2006; revised May 9, 2006; accepted May 27, 2006; published online June 15, 2006

Abstract

Promoter prediction has gained increased attention in studies related to transcriptional regulation of gene expression. We developed a web server named PMSearch (Poly Matrix Search) which utilizes Position Frequency Matrices (PFMs) to predict transcription factor binding sites (TFBSs) in DNA sequences. PMSearch takes PFMs (either user-defined or retrieved from local dataset which currently contains 507 PFMs from Transfac Public 7.0 and JASPAR) and DNA sequences of interest as the input, then scans the DNA sequences with PFMs and reports the sites of high scores as the putative binding sites. The output of the server includes 1) A plot for the distribution of predicted TFBS along the DNA sequence, 2) A table listing location, score and motif for each putative binding site, and 3) Clusters of predicted binding sites. PMSearch also provides links for accessing clusters of PFMs that are similar to the input PFMs to facilitate complicated promoter analysis.

Availability

PMSearch is available for free at http://www.nicemice.cn/bioinfo/PMS

Keywords

position frequency matrix; motif; transcription factor binding site; web server

Citation

Su et al., Bioinformation 1(5): 156-157 (2006)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.