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Compositional spectrum—revealing patterns for genomic sequence characterization and comparison

Author

Listed:
  • Kirzhner, Valery M.
  • Korol, Abraham B.
  • Bolshoy, Alexander
  • Nevo, Eviatar

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.

Suggested Citation

  • Kirzhner, Valery M. & Korol, Abraham B. & Bolshoy, Alexander & Nevo, Eviatar, 2002. "Compositional spectrum—revealing patterns for genomic sequence characterization and comparison," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 312(3), pages 447-457.
    • Handle: RePEc:eee:phsmap:v:312:y:2002:i:3:p:447-457
    DOI: 10.1016/S0378-4371(02)00843-9
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