Bioinformatics Vol. 17 no. 11 2001
Pages 1019-1026
© 2001 Oxford University Press
Combining frequency and positional information to predict transcription factor binding sites
basa *Innovationskolleg Theoretische Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 43, D-10115 Berlin, Germany
Received on December 10, 2000
; revised on April 27, 2001 and July 8, 2001
; accepted on July 25, 2001
Motivation: Even though a number of genome projects have been finished on the sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of those genes, rather weak signals of transcription factor binding sites may be detected.
Results: We introduce the new algorithm ITB, an Integrated Tool for Box finding, which combines frequency and positional information to predict transcription factor binding sites in upstream regions of coregulated genes. Motifs are extracted by exhaustive analysis of regular expression-like patterns and by estimating probabilities of positional clusters of motifs. ITB detects consensus sequences of experimentally verified transcription factor binding sites of the yeast Saccharomyces cerevisiae. Moreover, a number of new binding site candidates with significant scores are predicted. Besides applying ITB on yeast upstream regions, the program is run on human promoter sequences.
Availability: ITB is available upon request.
Contact: s.kielbasa{at}itb.biologie.hu-berlin.de
* Both authors contributed equally.
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