[Estimation of the quality of global alignment of amino acid sequences based on evolution criterion].

The aim of the work is to develop the common method for estimating the pairwise alignment quality versus the evolution distance (a degree of homology) between the sequences being comparing, and the type of the alignment procedure. 3D alignments as well as any data on 3D protein structure are not used in the study. Based on the accepted protein sequences evolution model it is possible to estimate the capability of the concrete alignment algorithm to recover the genuine alignment.

[A new approach to estimating the significance of identification of deletion inserts in pairwise alignment].

Within the framework of the unique method of estimating the significance of pairwise alignment of nucleotide sequences, developed by the authors, a new approach to the analysis of deletion inserts in pairwise alignment has been realized. It was shown that the decrease in the average integral length of deletion inserts in alignments obtained using the modern algorithms, as compared with true alignments, is related to a decrease in the number of some deletion inserts rather than a decrease in their average length.

[Effectiveness of a procedure for aligning sense sequences to make possible restoring the true alignment].

The method is presented which may estimate the reliability of any alignment procedure on the basis of comparing between genuine alignment obtained by generating of appropriate sequences with the result of alignment procedure work. The opportunities of the method are illustrated by testing the OPAL286 program. Dependence of reliability of the results i.