SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA

Background: Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limited to short ones or impose some constraints on the pattern type. Many patterns for binding sites in prokaryotic species are not well characterized but are known to be large, between 16–30 base pairs (bp) and contain at least 2 conserved bases. The length of prokaryotic species promoters (about 400 bp) and our interest in studying a small set of genes that could be a cluster of coregulated genes from microarray experiments led to the development of a new exhaustive algorithm targeting these large patterns. Results: We present Searchpattool, a new method to search for and select the most specific (conservative) frequent patterns. This method does not impose restrictions on the density or the structure of the pattern. The best patterns (motifs) are selected using several statistics, including a new application ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Fathi Elloumi, Martha Nason
• Keywords: BMCBI 2007, Computational Methods, Exhaustive Algorithms, Prokaryotic Species