TELKOMNIKA Indonesian Journal of Electrical Engineering
Vol 12, No 12: December 2014

Accelerating Computation of DNA Multiple Sequence Alignment in Distributed Environment


Satra, Ramdan ( Bogor Agricultural University ) , Kusuma, Wisnu Ananta ( Bogor Agricultural University ) , Sukoco, Heru ( Bogor Agricultural University )



Article Info

Publish Date
01 Dec 2014

Abstract

Multiple sequence alignment (MSA) is a technique for finding similarity in many sequences. This technique is very important to support many Bioinformatics task such as identifying Single Nucleotide Polymorphism (SNP) and metagenome fragments binning. The simplest algorithm in MSA is Star Algorithm. The complexity of DNA multiple sequence alignment using dynamic programming technique is very high. This research aims to accelerate computation of Star Mutiple Sequence Alignment using Message Passing Interfaces (MPI). The performance of the proposed method was evaluated by calculating speedup. Experiment was conducted using 64 sequences of 800 bp Glycine-max-chromosome-9-BBI fragments yielded by randomly cut from reference sequence of Glycine-max-chromosome-9-BBI taken from NCBI (National Center for Biotechnology Information). The results showed that the proposed technique could obtain speedup three times using five computers when aligning 64 sequences of Glycine-max-chromosome-9-BBI fragments.  Moreover, the increasing of the number of computers would significantly increased speedup of the proposed


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Original Source : http://www.iaesjournal.com/online/index.php/TELKOMNIKA/article/view/6572
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Journal Info

Abbrev

TELKOMNIKA

Publisher

Subject

Computer Science & IT Control & Systems Engineering Electrical & Electronics Engineering

Description

TELKOMNIKA Indonesian Journal of Electrical Engineering (ISSN: 2302-4046, e-ISSN: 2087-278X, a Ei Compendex Indexed journal) is a monthly peer reviewed International Journal in English. The aim of this journal is to publish high-quality articles dedicated to all aspects of the latest outstanding ...