FootPrinter: a program designed for phylogenetic footprinting

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

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 accurat...

MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes

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 most conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose in prokaryotic genomes, making use of the phylogenetic relationship...

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting ...

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Unrealistic phylogenetic trees may improve phylogenetic footprinting