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Phylogenetic footprinting: a boost for microbial regulatory genomics

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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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Acknowledgments

The authors acknowledge the DBT center for bioinformatics facility at Department of Bioscience and Biotechnology, Banasthali University, Banasthali, India for support.

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No competing financial interests exist.

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Authors and Affiliations

  1. Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, India

    Pramod Katara & Vinay Sharma

  2. Biotechnology Division, Defence Institute of Bio Energy Research, Goraparao, Haldwami, 263139, India

    Atul Grover

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  1. Pramod Katara
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  2. Atul Grover
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Correspondence to Pramod Katara.

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Katara, P., Grover, A. & Sharma, V. Phylogenetic footprinting: a boost for microbial regulatory genomics. Protoplasma 249, 901–907 (2012). https://doi.org/10.1007/s00709-011-0351-9

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