PhyloCon (Phylogenetic Consensus) combines phylogenetic data with coregulated genes to identify regulatory motifs. PhyloCon is a motif discovery program. It is derived from a well established program “Consensus”, with comparative genomic features added. PhyloCon assumes a “multiple gene, multiple species” model. It takes into account both conservation among orthologous genes and co-regulation of genes within a species. This algorithm first aligns conserved regions of orthologous sequences into multiple sequence alignments, or profiles, then compares profiles representing non-orthologous sequences. Motifs emerge as common regions in these profiles. The program will determine the width of the pattern being sought.
Stormo Lab in Department of Genetics, Washington University
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Bioinformatics. 2003 Dec 12;19(18):2369-80.
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
Wang T, Stormo GD.