WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

Background: This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. Results: We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Giulio Pavesi, Federico Zambelli, Graziano Pesole
• Keywords: BMCBI 2007, General Regulatory Regions, Homologous Genes, Transcription Factor