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Review
. 2012 Oct;249(4):901-7.
doi: 10.1007/s00709-011-0351-9. Epub 2011 Nov 24.

Phylogenetic footprinting: a boost for microbial regulatory genomics

Pramod Katara  1 , Atul Grover, Vinay Sharma
Affiliations
Review

Phylogenetic footprinting: a boost for microbial regulatory genomics

Pramod Katara et al. Protoplasma. 2012 Oct.

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.

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