Modification of the Smith-Waterman algorithm for local alignment of genetic sequences based on the window method

E. S. Bezuglova, E. M. Shiriaev, N. N. Kucherov, M. G. Babenko

North-Caucasus Federal University

Abstract: he paper presents a modified algorithm for local alignment of genetic sequences based on the Smith-Waterman algorithm, using window method and run-length encoding. an experimental comparison of the performance of the proposed approach with the classical algorithm by such metrics as execution time, average and peak memory usage is carried out. The results demonstrate the effectiveness of the modification while preserving the quality of alignment, especially in resource-constrained environments. The work has practical implications for bioinformatics tasks involving genome analysis, gene annotation and homologous site search.

Keywords: Smith-Waterman algorithm, run-length encoding, window method, genetic sequences, local alignment, bioinformatics.

DOI: 10.15514/ISPRAS-2025-37(5)-14