, Volume 53, Issue 4, pp 253–255 | Cite as

A new approach to assessing the validity of indels in algorithmic pair alignments

  • V. O. Polyanovsky
  • M. A. Roytberg
  • V. G. Tumanyan
Molecular Biophysics


Analysis of the structure of indels in algorithmic versus evolutionary alignments based on a set of inequalities confirms the conclusions from numerical modeling. For the more divergent sequences (PAM > 60), the tested aligning algorithm (SW) tends to increase the mean length of indels and decrease their number.

Key words

pairwise alignment insertion deletion 


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  1. 1.
    V. G. Tumanyan, L. E. Sotnikova, and A. V. Kholopov, Dokl. RAN 166, 1465 (1966).Google Scholar
  2. 2.
    V. V. Poroikov, N. G. Esipova, and V. G. Tumanyan, Mol. Biol. 18, 541 (1984).Google Scholar
  3. 3.
    T. F. Smith and M. S. Waterman. J. Mol. Biol. 147, 195 (1981).CrossRefGoogle Scholar
  4. 4.
    S. B. Needleman and C. D. Wunsch. J. Mol. Biol. 48, 443 (1970).CrossRefGoogle Scholar
  5. 5.
    S. F. Altschul, W. Gish, W. Miller, et al., J. Mol. Biol. 215, 403 (1990).Google Scholar
  6. 6.
    D. J. Lipman and W. R. Pearson, Science 227, 1435 (1985).CrossRefADSGoogle Scholar
  7. 7.
    V. O. Polyanovsky, E. Ya. Demchuk, and V. G. Tumanyan, Mol. Biol. 28, 1341 (1994).Google Scholar
  8. 8.
    V. O. Polyanovsky, M. A. Roytberg, and V. G. Tumanyan, J. Comput. Biol. 15, 379 (2008).CrossRefMathSciNetGoogle Scholar
  9. 9.
    M. Dayhoff, R. Schwartz, and B. Orcutt, in A model of evolutionary change in proteins, Ed. M. Dayhoff, Atlas of Protein Sequence and Structure (National Biomedical Research Foundation, Washington, 1978), pp. 345–352.Google Scholar
  10. 10.
    S. A. Benner, M. A. Cohen, and G. H. Gonnet, J. Mol. Biol. 229, 1065 (1993).CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2008

Authors and Affiliations

  • V. O. Polyanovsky
    • 1
  • M. A. Roytberg
    • 2
  • V. G. Tumanyan
    • 1
  1. 1.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
  2. 2.Institute of Mathematical Problems in BiologyRussian Academy of SciencesPushchino, Moscow RegionRussia

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