Rapid Estimates of Statistical Significance of the Pairwise Nucleotide Sequence Alignment

Statistical significance of the similarity observed is the main question while comparing sequences. This problem has not yet been solved mathematically for optimal aligning of the sequences containing insertions and deletions. We have carried out the regression analysis of the observed similarity of random sequences depending on their length and nucleotide composition and are proposing a practical method to estimate the probability of the similarity observed to be statistically significant. The regression parameters being determined for a given alignment scheme (similarity matrix and penalties for deletions) for a pair of nucleotide sequences, the statistical significance of the similarity observed can be precisely estimated basing on only their lengths and nucleotide composition.