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Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
Open accessAbstract
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.
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DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
Cited by
Sequencing and comparison of yeast species to identify genes and regulatory elements
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,753
Molecular Signatures of Natural Selection
Nielsen, R. (2005) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.112420 · Cited by 1,641
A survey of DNA motif finding algorithms
Das, M. K., & Dai, H.-K. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s7-s21 · Cited by 429
Goren, A., Ram, O., Amit, M., Keren, H., Lev-Maor, G., Vig, I., Pupko, T., & Ast, G. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.05.008 · Cited by 306
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Siddharthan, R., Siggia, E. D., & van Nimwegen, E. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010067 · Cited by 276
Metadata
- Authors
- Blanchette, M., & Tompa, M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-05-01
- Volume
- 12
- Issue
- 5
- Pages
- 739-748
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2041726559
- Cited by
- 327
- References
- 1
- Type
- posted content
- Language
- en
- Open access
- bronze
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