A multistep bioinformatic approach detects putative regulatory elements in gene promoters

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 sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of t...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Stefania Bortoluzzi, Alessandro Coppe, Andrea Bisognin, Cinzia Pizzi, Gian Antonio Danieli
• Keywords: BMCBI 2005, Promoter, Sequence Motifs, Sequences