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Nucleic Acids Research 2006 34(Web Server issue):W566-W570; doi:10.1093/nar/gkl285
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Giulio Pavesi1, Paolo Mereghetti2, Federico Zambelli1, Marco Stefani2, Giancarlo Mauri2 and Graziano Pesole1,3,4,*

1 Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milano Milano, Italy 2 Dipartimento di Informatica, Sistemistica e Comunicazione, University of Milano-Bicocca Milano, Italy 3 Dipartimento di Biochimica e Biologia Molecolare, University of Bari Bari, Italy 4 Istituto Tecnologie Biomediche—Consiglio Nazionale delle Ricerche Bari, Italy

*To whom correspondence should be addressed. Tel: +39 0250314915; Fax: +39 0805443317; Email: graziano.pesole{at}uniba.it

Received March 27, 2006. Accepted April 5, 2006.

Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. The server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites (TFBSs) in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved TFBSs and distal regulatory modules in sequences from homologous genes; RNAProfile, for the discovery of conserved secondary structure motifs in unaligned RNA sequences whose secondary structure is not known. In this way, a given gene can be compared with other co-regulated genes or with its homologs, or its mRNA can be analyzed for conserved motifs regulating its post-transcriptional fate. The web server thus provides researchers with different strategies and methods to investigate the regulation of gene expression, at both the transcriptional and post-transcriptional levels. Available at http://www.pesolelab.it/modtools/ and http://www.beacon.unimi.it/modtools/.


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