Title :
Parallelisation of sequence comparison algorithms using hybridised parallel techniques
Author :
Umar, Ibrahim ; Alqudami, Nasser ; Rashid, Nur Aini Abdul ; Abdullah, Rosni
Author_Institution :
Sch. of Comput. Sci., Univ. Sains Malaysia, Minden, Malaysia
Abstract :
The aim of this work is how to speed up the process of the biological (DNA and proteins) sequence comparison process by using a hybrid parallelisation technique of combining different parallel methods. Smith-Waterman algorithm has been known as the most optimal algorithm for doing the sequence comparison. Unfortunately, this algorithm is considered slow due to its quadratic time complexity. Multiple Instruction Multiple Data (MIMD), Single Instruction Multiple Data (SIMD), and Single Program Multiple Data (SPMD) methods were chosen because of their efficiency, wide-availability in off-the-shelf inexpensive machines and simple network distributed systems. Based on the results, the combined (hybrid) algorithm has succeeded in reducing the overall algorithm execution time.
Keywords :
bioinformatics; computational complexity; parallel algorithms; Smith-Waterman algorithm; biological sequence; hybrid parallelisation technique; hybridised parallel techniques; multiple instruction multiple data; quadratic time complexity; sequence comparison algorithms; single instruction multiple data; single program multiple data; Bioinformatics; Biology computing; Concurrent computing; DNA; Databases; Diseases; Hardware; Parallel architectures; Parallel machines; Protein sequence; Bioinformatics; Distributed Systems; MPI; OpenMP (key words); Parallel; SIMD; Sequence Comparison; Smith-Waterman;
Conference_Titel :
High-Capacity Optical Networks and Enabling Technologies (HONET), 2009 6th International Symposium on
Conference_Location :
Alexandria
Print_ISBN :
978-1-4244-5992-6
DOI :
10.1109/HONET.2009.5423077
