The Locally Optimal Method of Cyclic Alignment to Reveal Latent Periodicities in Genetic Texts: the NAD-binding Protein Sites View Full Text


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Article Info

DATE

2003-07

AUTHORS

A. A. Laskin, E. V. Korotkov, M. B. Chaley, N. A. Kudryashov

ABSTRACT

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying apparent regularity in their secondary structures, not being obvious at the primary structure level. More... »

PAGES

561-570

References to SciGraph publications

  • 1999-06. Latent Periodicity of Protein Sequences in JOURNAL OF MOLECULAR MODELING
  • 1974-07. Chemical and biological evolution of a nucleotide-binding protein in NATURE
  • 1999-06. The protein data bank in GENETICA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1023/a:1025139427862

    DOI

    http://dx.doi.org/10.1023/a:1025139427862

    DIMENSIONS

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