Open AccessParallel implementation of the primer search algorithm for loop-mediated isothermal amplification
Author(s) -
Л.У. Ахметзянова,
Т.М. Давлеткулов,
I. M. Gubaydullin,
A R Islamgulov
Publication year - 2021
Publication title -
journal of physics. conference series
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.21
H-Index - 85
eISSN - 1742-6596
pISSN - 1742-6588
DOI - 10.1088/1742-6596/2131/2/022004
Subject(s) - loop mediated isothermal amplification , primer (cosmetics) , computer science , thread (computing) , algorithm , search algorithm , dna , biology , genetics , programming language , chemistry , organic chemistry
In the paper, the implementation of an algorithm of search for primers in a DNA sequence with a size varying between one nucleotide and multiple million nucleotides was discussed. This analysis was done within the objective of finding a set of six specific primers that are used for a conduction of the loop-mediated isothermal amplification (LAMP). For the fastest search result possible, a parallel search for the primer with the use of the Rabin-Karp Algorithm which enables the search for a primer’s entry in DNA sequence in each thread was proposed. A new software for search for primers was developed using Python with BioPython library which implements the algorithm.