Identification of Transcription Factor Binding Sites in Streptomyces coelicolor A3(2) by Phylogenetic Comparison

The first step consists in running BLASTP [2] on each pair of genomes of a selected sample of related bacteria, in order to find putative orthologous genes between every pair of organisms. Besides the genome of interest (S. coelicolor), the sample included Streptomyces avermitilis, Mycobacterium tuberculosis, Mycobacterium leprae and Corynebacterium glutamicum. The goal of pairwise comparison of all species is to establish groups of orthologous genes present in all those bacteria. Obtained groups of orthologous gene sequences are then filtered according to the e-value and/or length differences and/or sequence identity level, and then processed as explained on Figure 2. This treatment results in a file grouping on each line the identifiers of putative orthologous genes for each bacteria. DNA 5’ 5’ 3’ 3’ genes