Increasing the Accuracy of Global Alignment of Amino Acid Sequences by Constructing a Set of Alignment Candidates

摘要

The accuracy of global Smith–Waterman alignments and Pareto-optimal alignments depending on the degree of sequence similarity (percent of coincidence, %id, and the number of removed fragments NGap) has been examined. An algorithm for constructing a set of three to six alignments has been developed of which the best alignment on the average exceeds in accuracy the best alignment that can be constructed using the Smith–Waterman algorithm. For weakly homologous sequences (%id 15, NGap 20), the increase in accuracy is on the average about 8%, with the average accuracy of the global Smith–Waterman alignments being about 38% (the accuracy was estimated on model test sets).