title: The average mutual information profile as a genomic signature.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Electrical Engineering, University of Nebraska, Lincoln, NE USA. mark@engr.unl.edu
authors.forename: Mark
authors.initials: M
authors.lastname: Bauer
authors.forename: Sheldon M
authors.initials: SM
authors.lastname: Schuster
authors.forename: Khalid
authors.initials: K
authors.lastname: Sayood
mesh_terms: D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D007257:Information Theory; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*