FootPrinter: a program designed for phylogenetic footprinting

FootPrinter: a program designed for phylogenetic footprinting

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 ...

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Unrealistic phylogenetic trees may improve phylogenetic footprinting

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 ...