Parallel Fast Dynamic Algorithm for Sequence Alignment Using OpenMP and Partitioning Scheme

Abstract

Sequence alignment process considered one of the most important tasks in bioinformatic. There are two types of alignment pairwise and multiple sequence alignment. Many algorithms proposed to complete this task. The key parameter in these algorithms is alignment and its scoring value. If the proposed algorithm maximizes the score, so it will be optimal. The algorithms used to align sequences have two main drawbacks. The first is the sensitivity when the data used is very large, the output score is not optimal and has a bad sensitivity. The second is the execution time when the data is large. To overcome these two problems the parallel version of Fast Dynamic Algorithm for Pairwise sequence Alignment is proposed. The first problem solved by partitioning scheme and the second solved by using OpenMP to distribute tasks on available threads. The results indicated that the proposed parallel Algorithms achieve high level of accuracy and sensitivity and improve the execution time. Keywords—Sequence alignment, optimal score, Fast Dynamic Algorithm for Pairwise Sequence Alignment, OpenMP