Identification of compositionally distinct regions in genomes using the centroid method.
BACKGROUND
It is known that most genomic regions of special interest, e.g. horizontally acquired sequences, genomic islands, etc. have distinct word (m-mer) compositions. Most of the earlier work along this direction, addressed di- and tri-nucleotide compositions. We present an approach that can be applied to analyze compositions of any given word size. The method, called the centroid approach, can reveal compositionally distinct regions in genomic sequences for any given word size.


RESULTS
We applied our method to 50 bacterial genomes and demonstrated its ability to identify embedded sequences of varying lengths from distantly related organisms. We also investigated the genetic makeup of the regions identified as compositionally distinct by our method, for four organisms from our dataset. Pathogenicity island (PAI) components and genes encoding strain-specific proteins are all frequently seen to be constituents of these regions.


BACKGROUND
Program is available on request from the authors.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Rajan
Issaac
I
Life Sciences Research, Advanced Technology Centre, Tata Consultancy Services, Hyderabad 500 081, Andhra Pradesh, India.
Aravamuthan
Sarang
S
Mande
Sharmila S
SS
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D037521:Virulence Factors / Q000235:genetics*
D037521:Virulence Factors