A multistep bioinformatic approach detects putative regulatory elements in gene promoters.

ABSTRACT:

Background

Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs.

Results

Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated

SUBMITTER: Bortoluzzi S 

PROVIDER: S-EPMC1173081 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature