[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.e. reconstruction of genuine alignment from percent of mutations and deletion-insertions are pointed. The method developed provides correct optimal choice of parameters for alignment procedure in the sense of reliability and probability of correct reconstruction of the original alignment.