title: Phylogenetic footprinting: a boost for microbial regulatory genomics.
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. There are two popular sets of methods-alignment-based and motif-based, which are generally employed for phylogenetic methods. However, serious efforts have lacked to develop a tool exclusively for phylogenetic footprinting, based on either of these methods. Nevertheless, a number of software and tools exist that can be applied for prediction of phylogenetic footprinting with variable degree of success. The output from these tools may get affected by a number of factors associated with current state of knowledge, techniques and other resources available. We here present a critical apprehension of various phylogenetic approaches with reference to prokaryotes outlining the available resources and also discussing various factors affecting footprinting in order to make a clear idea about the proper use of this approach on prokaryotes.
authors: Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, India. pmkatara@gmail.com
authors: Pramod
authors: P
authors: Katara
authors: Atul
authors: A
authors: Grover
authors: Vinay
authors: V
authors: Sharma
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001665:Binding Sites; D018983:DNA Footprinting / Q000379:methods*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D010802:Phylogeny