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
. 2003 Jul 1;31(13):3840-2.
doi: 10.1093/nar/gkg606.

FootPrinter: A program designed for phylogenetic footprinting

Mathieu Blanchette  1 , Martin Tompa
Affiliations

FootPrinter: A program designed for phylogenetic footprinting

Mathieu Blanchette et al. Nucleic Acids Res. .

Abstract

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Sample FootPrinter output on the upstream regions of nine growth hormone genes. We searched for motifs of size 8 with at most two mutations. Motif losses were allowed, at a cost of one mutation. The subregion size was set to 100 bp with a subregion change cost of one mutation. The motif list reported on the right has been trimmed to fit on the page.
See this image and copyright information in PMC

References

    1. Tagle D., Koop,B., Goodman,M., Slightom,J., Hess,D. and Jones,R. (1988) Embryonic ɛ and γ globin genes of a prosimian primate (Galago crassicaudatus); nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol., 203, 439–455. - PubMed
    1. Duret L. and Bucher,P. (1997) Searching for regulatory elements in human noncoding sequences. Curr. Op. Struct. Biol., 7, 399–405. - PubMed
    1. Blanchette M., Schwikowski,B. and Tompa,M. (2002) Algorithms for phylogenetic footprinting. J. Comput. Biol., 9, 211–223. - PubMed
    1. Blanchette M. and Tompa,M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739–748. - PMC - PubMed
    1. Blanchette M., Kwong,S. and Tompa,M. (2003) An empirical comparison of tools for phylogenetic footprinting. In Third IEEE Symposium on Bioinformatics and Bioengineering, IEEE Press, Los Alamitos, CA, pp. 69–78.

Publication types