Biophysics

, 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

Abstract

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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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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