Scientific journal
Scientific Review. Technical science
ISSN 2500-0799
ПИ №ФС77-57440

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PARALLEL GLOBAL ALIGNMENT ALGORITHM WITH THE OPTIMAL USE OF MEMORY

Abu-Khalil Z.M. 1 Morylev R.I. 1 Steinberg B.Y. 1
1 Southern Federal University
The article refers to a relatively young and rapidly evolving scientific discipline bioinformatics, and presents another algorithm of global alignment of two nucleotide sequences. Global alignment algorithms are the bases of many metrics in spaces of nucleotide sequences, and are used to construct phylogenetic trees. This algorithm differs from known ones because it is adapted to parallelization for multi-core processors and accelerators. Our implementation is designed; the results of numerical experiments are presented in this paper. Another difference of this algorithm is the ability to adapt to the amount of available memory. This algorithm uses procedures of two known algorithms: Hirschberg and Needleman-Wunsch. This allows us to achieve the best result within used memory constraints.