FootPrinter

Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences[1, 2, 3, 4]. For more information and a download, see here.

References

1. Blanchette M and Tompa M. FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res. 2003 Jul 1;31(13):3840-2.
2. Fang F and Blanchette M. FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W617-20. DOI:10.1093/nar/gkl123 |
3. Blanchette M and Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 2002 May;12(5):739-48. DOI:10.1101/gr.6902 |
4. Blanchette M, Schwikowski B, and Tompa M. Algorithms for phylogenetic footprinting. J Comput Biol. 2002;9(2):211-23. DOI:10.1089/10665270252935421 |