Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2002 May;12(5):739-48.
doi: 10.1101/gr.6902.

Discovery of regulatory elements by a computational method for phylogenetic footprinting

Mathieu Blanchette  1 , Martin Tompa
Affiliations
Comparative Study

Discovery of regulatory elements by a computational method for phylogenetic footprinting

Mathieu Blanchette et al. Genome Res. 2002 May.

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
FootPrinter identified 12 highly conserved motifs in the metallothionein gene family. Each input sequence is the 590 bp located upstream of the start codon. For more details on each motif, see Table 1. The phylogenetic tree is derived from Binz and Kägi (1997; branch lengths not to scale). Numbers along branches indicate when each motif was created (unboxed) or lost (boxed), ignoring any less conserved occurrences of the motif not reported by FootPrinter.
See this image and copyright information in PMC

References

    1. Bailey TL, Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning. 1995;21:51–80.
    1. Binz P-A, Kägi JHR. Molecular evolution of metallothioneins: Contributions from coding and non-coding regions. Poster at the Second European Meeting of the Protein Society, Cambridge. 1997.
    1. Blanchette, M., Schwikowski, B., and Tompa, M. 2002. Algorithms for phylogenetic footprinting. J. Comput. Biol. (in press). - PubMed
    1. Buhler J, Tompa M. Finding motifs using random projections. In: Lengauer T, Sankoff D, Istrail S, Pevzner P, Waterman M, editors. Proceedings of the Fifth Annual International Conference on Computational Biology. 2001. pp. 69–76. . Montreal, Canada.
    1. Cliften P, Hillier L, Fulton L, Graves T, Miner T, Gish W, Waterston R, Johnston M. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 2001;11:1175–1186. - PubMed

Publication types

LinkOut - more resources