Randomised sequential and parallel algorithms for efficient quorum planted motif search

Abstract

Motifs are crucial patterns in biological sequences that have numerous applications. Motif search is an important step in obtaining meaningful patterns from biological data. However, most of the existing algorithms are deterministic and the role of randomisation in this area is still unexploited. This paper focuses on (l,d)-motif model, which is also known as Planted Motif Search (PMS) and proposes an efficient randomised algorithm, named qPMS10, to solve PMS. We utilise the most efficient PMS solver until now, named qPMS9, as a subroutine. We analyse the time complexity of both algorithms and provide a performance comparison of qPMS10 with qPMS9 on standard benchmark datasets. In addition, we offer a parallel implementation of qPMS10 and run tests using up to four processors. Both theoretical and empirical analyses demonstrate that our randomised algorithm outperforms the existing algorithms for solving PMS.