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Comining phylogenetic data with co-regulated genes to identify regulatory motif (2003)
| Venue: | BIOINFORMATICS |
| Citations: | 136 - 11 self |
BibTeX
@MISC{Wang03cominingphylogenetic,
author = {Ting Wang and Gary D. Stormo},
title = {Comining phylogenetic data with co-regulated genes to identify regulatory motif},
year = {2003}
}
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Abstract
Motivation: Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Two categories of algorithms have been developed to identify common motifs from a set of DNA sequences. The first can be called a ‘multiple genes, single species’approach. It proposes that a degenerate motif is embedded in some or all of the otherwise unrelated input sequences and tries to describe a consensus motif and identify its occurrences. It is often used for co-regulated genes identified through experimental approaches. The second approach can be called ‘single gene, multiple species’. It requires orthologous input sequences and tries to identify unusually well conserved regions by phylogen-etic footprinting. Both approaches perform well, but each has some limitations. It is tempting to combine the knowledge of co-regulation among different genes and conservation among orthologous genes to improve our ability to identify motifs. Results: Based on the Consensus algorithm previously established by our group, we introduce a new algorithm called PhyloCon (Phylogenetic Consensus) that 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. Here we present a novel statistic to compare profiles of DNA sequences and a greedy approach to search for common subprofiles. We demonstrate that PhyloCon performs well on both synthetic and biological data. Availability: Software available upon request from the authors.
Keyphrases
regulatory motif co-regulated gene phylogenetic data dna sequence orthologous gene second approach common region experimental approach different gene biological data phylogen-etic footprinting phylocon performs common subprofiles phylogenetic consensus novel statistic computational biology unrelated input sequence common motif non-orthologous sequence degenerate motif single specie orthologous input sequence conserved region single gene greedy approach consensus motif multiple gene multiple sequence alignment new algorithm unaligned dna sequence fundamental problem multiple specie motif emerge orthologous sequence
