A large-scale comparison of genomic sequences: one promising approach.
We introduce a novel, linguistic-like method of genome analysis. We propose a natural approach to characterizing genomic sequences based on occurrences of fixed length words from a predefined, sufficiently large set of words (strings over the alphabet [A, C, G, T]). A measure based on this approach is called compositional spectrum and is actually a histogram of imperfect word occurrences. Our results assert that the compositional spectrum is an overall characteristic of a long sequence i.e., a complete genome or an uninterrupted part of a chromosome. This attribute is manifested in the similarity of spectra obtained on different stretches of the same genome, and simultaneously in a broad range of dissimilarities between spectral representations of different genomes. High flexibility characterizes this approach due to imperfect matching and as a result sets of relatively long words can be considered. The proposed approach may have various applications in intra- and intergenomic sequence comparisons.
Kirzhner
Valery
V
Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel. valery@esti.haifa.ac.il
Nevo
Eviatar
E
Korol
Abraham
A
Bolshoy
Alexander
A
D000465:Algorithms; D000818:Animals; D001105:Archaea / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D005051:Eubacterium / Q000235:genetics; D005057:Eukaryotic Cells; D023281:Genomics; D006801:Humans; D008037:Linguistics; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D013223:Statistics as Topic / Q000379:methods*
D004247:DNA