The Average Mutual Information Profile as a Genomic Signature

Mark Bauer¹ , Sheldon M Schuster² and Khalid Sayood¹

¹Department of Electrical Engineering, University of Nebraska, Lincoln, NE USA

²Keck Graduate Institute, Claremont Colleges, Claremont, CA, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:48doi:10.1186/1471-2105-9-48


Published:	25 January 2008

Abstract

Background

Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discriminating organisms using genomic data. Species specific genomic signatures are useful in a variety of contexts such as evolutionary analysis, assembly and classification of genomic sequences from large uncultivated microbial communities and a rapid identification system in health hazard situations.

Results

We have analyzed genomic sequences of eukaryotic and prokaryotic chromosomes as well as various subtypes of viruses using an information theoretic framework. We confirm the existence of a species specific average mutual information (AMI) profile. We use these profiles to define a very simple, computationally efficient, alignment free, distance measure that reflects the evolutionary relationships between genomic sequences. We use this distance measure to classify chromosomes according to species of origin, to separate and cluster subtypes of the HIV-1 virus, and classify DNA fragments to species of origin.

Conclusion

AMI profiles of DNA sequences prove to be species specific and easy to compute. The structure of AMI profiles are conserved, even in short subsequences of a species' genome, rendering a pervasive signature. This signature can be used to classify relatively short DNA fragments to species of origin.