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

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).

[1]  S. Salzberg,et al.  Alignment of whole genomes. , 1999, Nucleic acids research.

[2]  M. Q. Zhang.  Large-scale gene expression data analysis: a new challenge to computational biologists. , 1999, Genome research.

[3]  Enno Ohlebusch,et al.  Efficient multiple genome alignment , 2002, ISMB.

[4]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[5]  Xavier Messeguer,et al.  PROMO: detection of known transcription regulatory elements using species-tailored searches , 2002, Bioinform..

[6]  P. Bucher.  Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. , 1990, Journal of molecular biology.

[7]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[8]  L. Kedes,et al.  Muscle-specific expression of the cardiac alpha-actin gene requires MyoD1, CArG-box binding factor, and Sp1. , 1990, Genes & development.

[9]  Nicolas Mermod,et al.  Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA , 1998, Silico Biol..

[10]  S. Salzberg,et al.  Fast algorithms for large-scale genome alignment and comparison. , 2002, Nucleic acids research.

[11]  Xavier Messeguer Peypoch,et al.  Efficient space and time multicomparison of genomes , 2003 .

[12]  J. Casacuberta,et al.  Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. , 2002, Molecular biology and evolution.