Compositional spectrum—revealing patterns for genomic sequence characterization and comparison

Valery M. Kirzhner, Abraham B. Korol, Alexander Bolshoy and Eviatar Nevo

Physica A: Statistical Mechanics and its Applications, 2002, vol. 312, issue 3, 447-457

Abstract: In this paper we propose a natural approach to characterizing genomic sequences, based on occurrences of fixed length words (strings over the alphabet {A,C,G,T}) from a sufficiently large set W of arbitrary (in general case) words. According to our approach, any genomic sequence can be characterized by a histogram of frequencies of imperfect matching of words from the set W that is called a compositional spectrum (CS). The specificity of CSs is manifest in a reasonable similarity of spectra obtained on different stretches of the same genome and, simultaneously, in a broad range of dissimilarities between spectral characteristics of different genomes. The proposed approach may have various applications in intra- and intergenomic sequence comparisons.

Keywords: DNA sequences; Set of words; Sequence comparisons; Compositional spectra; Imperfect matching (search for similar items in EconPapers)
Date: 2002
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:312:y:2002:i:3:p:447-457

DOI: 10.1016/S0378-4371(02)00843-9

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