Yakovlev, P. A. Fast trie-based method for multiple pairwise sequence alignment. (English. Russian original) Zbl 1416.92134 Dokl. Math. 99, No. 1, 64-67 (2019); translation from Dokl. Akad. Nauk, Ross. Akad. Nauk 484, No. 4, 401-404 (2019). Summary: A method for efficient comparison of a symbol sequence with all strings of a set is presented, which performs considerably faster than the naive enumeration of comparisons with all strings in succession. The procedure is accelerated by applying an original algorithm combining a prefix tree and a standard dynamic programming algorithm searching for the edit distance (Levenshtein distance) between strings. The efficiency of the method is confirmed by numerical experiments with arrays consisting of tens of millions of biological sequences of variable domains of monoclonal antibodies. MSC: 92D20 Protein sequences, DNA sequences 68Q25 Analysis of algorithms and problem complexity Keywords:multiple pairwise sequence alignment; biological sequences × Cite Format Result Cite Review PDF Full Text: DOI References: [1] Levenshtein, V. I., No article title, Dokl. Akad. Nauk SSSR, 163, 845 (1965) [2] Needleman, S. B.; Wunsch, C. D., No article title, J. Mol. Biol., 48, 443-453 (1970) · doi:10.1016/0022-2836(70)90057-4 [3] Damerau, F. J., No article title, Commun. ACM, 7, 171-176 (1964) · doi:10.1145/363958.363994 [4] Smith, T. F.; Waterman, M. S., No article title, J. Mol. Biol., 147, 195-197 (1981) · doi:10.1016/0022-2836(81)90087-5 [5] Brudno, M., No article title, Bioinformatics, 19, 54-62 (2003) · doi:10.1093/bioinformatics/btg1005 [6] Wagner, R. A.; Fischer, M. J., No article title, J. ACM, 21, 168-173 (1974) · Zbl 0278.68032 · doi:10.1145/321796.321811 [7] Aho, A. V.; Corasick, M. J., No article title, Commun. ACM, 18, 333-340 (1975) · Zbl 0301.68048 · doi:10.1145/360825.360855 [8] Cohen, J. D., No article title, ACM Trans. Inf. Syst., 15, 291-320 (1997) · doi:10.1145/256163.256168 [9] Market, E.; Papavasiliou, F. N., No article title, PLoS Biol., 1, 24-27 (2003) · doi:10.1371/journal.pbio.0000016 This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.