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Nucleic Acids Research Advance Access originally published online on May 31, 2009
Nucleic Acids Research 2009 37(Web Server issue):W247-W252; doi:10.1093/nar/gkp464
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W247-W252
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

Federico Zambelli1, Graziano Pesole2,3 and Giulio Pavesi1,*

1Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, 2Dipartimento di Biochimica e Biologia Molecolare ‘E. Quagliariello’, University of Bari and 3Istituto Tecnologie Biomediche—Consiglio Nazionale delle Ricerche, Bari, Italy

*To whom correspondence should be addressed. Tel: +39 02 503 14884; Fax: +39 02 503 15044; Email: giulio.pavesi{at}unimi.it

Received March 4, 2009. Revised May 4, 2009. Accepted May 16, 2009.

The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time. The website is free and open to all users and there is no login requirement. Address: http://www.beaconlab.it/pscan.


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