Application of the Aho-Korasik Algorithm for the Selection of Primers for Loop Isothermal Amplification

Abstract

This paper presents a program which allows user to do primer design for identifying DNA target site or a whole genome with a goal of performing loopmediated isothermal amplification. The review of the most popular existing primer design programs for LAMP is carried out. Recommended conditions are presented in the paper. They are required to be taken in consideration during the process of primer design for loop-mediated isothermal amplification. These are the conditions: primer’s length, GC-content, amplicon average size, annealing temperature and distance between primers. A search for primer positions in genome is needed since loop-mediated isothermal amplification requires primer kits that consist of 6 primers in order for primer design to be done. The Aho–Corasick algorithm was proposed for a search implementation. This algorithm is capable of simultaneous search for a number of sample (primer) entries in a longer sequence (a fragment or a whole genome). This software allows the search for primers in genomes of various length and it groups primers by kits, which in turn could be applied in laboratory experiments. These kits are formed according both to the recommended conditions of primer selection for performing loop-mediated isothermal amplification and to the initial conditions, which are determined by the user before the process. After that, the user may choose the best option for their case from a list of primer kits that are being created as a result of performed computer analysis. The test run of the program was done during the search for a specific primer kit that is meant to be used for performing loop-mediated isothermal amplification of genome with a goal of detection of novel coronavirus infection SARS-CoV-2, a virus that triggers a dangerous disease, COVID-19. The software was developed using Python with BioPython and Pyahocorasick libraries and available at the link: https://cloud.mail.ru/public/C7av/QCkSiUomz.