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Nucleic Acids Research, 2003, Vol. 31, No. 13 3651-3653
© 2003 Oxford University Press

Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN

Domènec Farré, Romà Roset1, Mario Huerta2, José E. Adsuara2, Llorenç Roselló2, M. Mar Albà3 and Xavier Messeguer*,1,2

Computing Unit, Institut de Recerca Oncològica, L'Hospitalet, Spain 1 CEPBA-IBM Research Institute, Universitat Politècnica de Catalunya, Barcelona, Spain 2 Algorithmics and Genetics Group, Software Department, Universitat Politècnica de Catalunya, Barcelona, Spain 3 Biomedical Informatics Research Group, Health and Experimental Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain

*To whom correspondence should be addressed at Algorithmics and Genetics Group, Software Department, Universitat Politècnica de Catalunya, Jordi Girona 1-3, C6-117, Barcelona 08034, Spain. Tel: +34 93 4017333; Fax: +34 93 4017014; Email: messeguer{at}lsi.upc.es

In this paper we present several web-based tools to identify conserved patterns in sequences. In particular we present details on the functionality of PROMO version 2.0, a program for the prediction of transcription factor binding site in a single sequence or in a group of related sequences and, of MALGEN, a tool to visualize sequence correspondences among long DNA sequences. The web tools and associated documentation can be accessed at http://www.lsi.upc.es/~alggen (RESEARCH link).


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