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PMID: 11997340 Published · ppublish English Comparative Study Letter Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Genome research ·Vol. 12 ·No. 5 ·2002-05-00 ·Pages 739-48

Blanchette M, Tompa M

Abstract

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

MeSH Terms
Algorithms Animals Computational Biology/methods DNA Footprinting/methods Fish Proteins Genes, fos/genetics Genes, myc/genetics Growth Hormone/genetics Humans Insulin/genetics Interleukin-3/genetics Introns/genetics Metallothionein/genetics Multigene Family/genetics Phylogeny Promoter Regions, Genetic/genetics Regulatory Sequences, Nucleic Acid/genetics
Chemicals
Fish Proteins Insulin Interleukin-3 growth hormone type I, Salmo salar Growth Hormone Metallothionein
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Blanchette Mathieu
Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195-2350, USA.
Tompa Martin
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.6902
Published
2002-05-00
Pages
739-48
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC186562
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.6902 PMC Full Text View journal details
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