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Bioinformatics Vol. 18 no. 2 2002
Pages 333-334
© 2002 Oxford University Press

Applications Note

PROMO: detection of known transcription regulatory elements using species-tailored searches

Xavier Messeguer 1, Ruth Escudero 1, Domènec Farré 1, Oscar Núñez 1, Javier Martínez 1 and M.Mar Albà 2,*

1 Algorithmics and Genetics Group, Software Department, Universitat Politècnica de Catalunya, C/Jordi Girona Salgado, 1–3, 08034 Barcelona, Spain
2 Virus Genomics and Bioinformatics, Wohl Virion Centre, Department of Immunology and Molecular Pathology, University College London, 46 Cleveland St, London W1T 4JF, UK

Received on June 5, 2001 ; revised on August 3, 2001 ; accepted on September 12, 2001

Summary: We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences.

Availability: PROMO can be accessed online at http://www.lsi.upc.es/~alggen under the research link.

Supplementary information: An example of the graphic interface (Figure 1) can be visualized at http://www.lsi.upc.es/~alggen/recerca/promo/figuraBioinformatics.html.

Contact: peypoch{at}lsi.upc.es; m.alba{at}ucl.ac.uk

* To whom correspondence should be addressed.


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