Unrealistic phylogenetic trees may improve phylogenetic footprinting.

ABSTRACT:

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 requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily.

Results

Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprintin

SUBMITTER: Nettling M 

PROVIDER: S-EPMC5447242 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature