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

—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.