Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
Open Access
- 1 May 2002
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 12 (5) , 739-748
- https://doi.org/10.1101/gr.6902
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.Keywords
This publication has 37 references indexed in Scilit:
- Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprintsPublished by Elsevier ,2004
- Algorithms for Phylogenetic FootprintingJournal of Computational Biology, 2002
- The Sheep Genome Contributes to Localization of Control Elements in a Human Gene with Complex Regulatory MechanismsGenomics, 2001
- Identifying Functional Elements by Comparative DNA Sequence Analysis: Figure 1.Genome Research, 2001
- Human-mouse genome comparisons to locate regulatory sitesNature Genetics, 2000
- Computational identification of Cis -regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae 1 1Edited by F. E. CohenJournal of Molecular Biology, 2000
- Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitationNature Biotechnology, 1998
- Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 1Edited by G. von HeijneJournal of Molecular Biology, 1998
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Locating the vertices of a steiner tree in an arbitrary metric spaceMathematical Programming, 1975