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Publication : Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology

An exact algorithm to identify motifs in orthologous sequences from multiple species

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology - 01 Jan 2000

Blanchette M, Schwikowski B, Tompa M

Link to Pubmed [PMID] – 10977064

Proc Int Conf Intell Syst Mol Biol 2000;8:37-45

The identification of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the following approach to identifying motifs: given a collection of orthologous sequences from multiple species related by a known phylogenetic tree, search for motifs that are well conserved (according to a parsimony measure) in the species. We present an exact algorithm for solving this problem. We then discuss experimental results on finding promoters of the rbcS gene for a family of 10 plants, on finding promoters of the adh gene for 12 Drosophila species, and on finding promoters of several chloroplast encoded genes.