Accelerating Computation of DNA Multiple Sequence Alignment in Distributed Environment
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....
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| Main Authors: | , , |
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| Format: | EJournal Article |
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Institute of Advanced Engineering and Science,
2014-12-01.
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| Online Access: | Get fulltext |
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| LEADER | 02479 am a22003013u 4500 | ||
|---|---|---|---|
| 001 | ijeecs3946_2484 | ||
| 042 | |a dc | ||
| 100 | 1 | 0 | |a Satra, Ramdan |e author |
| 100 | 1 | 0 | |e contributor |
| 700 | 1 | 0 | |a Kusuma, Wisnu Ananta |e author |
| 700 | 1 | 0 | |a Sukoco, Heru |e author |
| 245 | 0 | 0 | |a Accelerating Computation of DNA Multiple Sequence Alignment in Distributed Environment |
| 260 | |b Institute of Advanced Engineering and Science, |c 2014-12-01. | ||
| 520 | |a 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. http://dx.doi.org/10.11591/telkomnika.v12i12.6572 | ||
| 540 | |a Copyright (c) 2014 Institute of Advanced Engineering and Science | ||
| 540 | |a http://creativecommons.org/licenses/by-nc-nd/4.0 | ||
| 546 | |a eng | ||
| 690 | |a Faculty of Mathematics and Natural Sciences; Computer Science | ||
| 690 | |a DNA multiple sequence alignment; distributed computing; star algorithm; message passing interface | ||
| 655 | 7 | |a info:eu-repo/semantics/article |2 local | |
| 655 | 7 | |a info:eu-repo/semantics/publishedVersion |2 local | |
| 655 | 7 | |2 local | |
| 786 | 0 | |n Indonesian Journal of Electrical Engineering and Computer Science; Vol 12, No 12: December 2014; 8278-8285 | |
| 786 | 0 | |n 2502-4760 | |
| 786 | 0 | |n 2502-4752 | |
| 786 | 0 | |n 10.11591/ijeecs.v12.i12 | |
| 787 | 0 | |n https://ijeecs.iaescore.com/index.php/IJEECS/article/view/3946/2484 | |
| 856 | 4 | 1 | |u https://ijeecs.iaescore.com/index.php/IJEECS/article/view/3946/2484 |z Get fulltext |