An efficient multicore implementation of planted motif problem

Abstract

In this paper we propose a parallel algorithm for the planted motif problem that arises in computational biol

PMS6MC: A multicore algorithm for motif discovery

“…The planted motif was then randomly mutated in exactly d randomly chosen positions. For each (l, d) value up to (19,7), we generated 20 instances and for larger (l, d) values, we generated 5 instances. The average run times for each (l, d) value are reported in this section.…”

Ứng Dụng Giải Thuật Song Song Trên Hệ Thống Cpu-Gpu Cho Bài Toán Tìm Kiếm Motif

“…Thuật toán BitBased ban đầu được đề xuất cho CPU [5], nó đã giải quyết bài toán tìm kiếm motif với l = 21 và số đột biến k = 8 trong 1,1 giờ.…”

High performance implementation of planted motif problem using suffix trees

“…The candidate motifs are then filtered out by checking if they are present in the remaining (n-n') sequences. This approach had been previously used in [11], [12]. Unlike in [11], the main purpose of using filtering is not to reduce memory requirement but to improve performance.…”

“…This approach had been previously used in [11], [12]. Unlike in [11], the main purpose of using filtering is not to reduce memory requirement but to improve performance. With decrease in number of sequences used for construction of suffix tree, the number of tree nodes decreases and so the size of occurrence list also decreases.…”

“…A recently proposed parallel approach, BitBased, is based on working with bitarrays, and can be effectively parallelized on multicore and GPU architectures [11] [12]. However, the memory requirement is a bottleneck in this approach for solving (l,d) PMP problems as l and d increase.…”