CFP last date
20 January 2025
Call for Paper
February Edition
IJCA solicits high quality original research papers for the upcoming February edition of the journal. The last date of research paper submission is 20 January 2025

Submit your paper
Know more
The week's pick
Responsive image
SFLA-Based Line Balancing and Task Optimization in Master-Slave Controlled Hanger Transportation Systems for Garment Production

Duc Hoang Nguyen
Random Articles
Reseach Article

Multiple Sequence Alignments with Parallel Computing

Published on March 2014 by Charu Sharma, Pankaj Agrawal, Preeti Gupta
journal_cover_thumbnail

International Conference on Advances in Computer Engineering and Applications
Foundation of Computer Science USA
ICACEA - Number 5
March 2014
Authors: Charu Sharma, Pankaj Agrawal, Preeti Gupta
d5824ea7-3020-439c-bb6a-5f9800da1496

Charu Sharma, Pankaj Agrawal, Preeti Gupta . Multiple Sequence Alignments with Parallel Computing. International Conference on Advances in Computer Engineering and Applications. ICACEA, 5 (March 2014), 16-21.

@article{
author = { Charu Sharma, Pankaj Agrawal, Preeti Gupta },
title = { Multiple Sequence Alignments with Parallel Computing },
journal = { International Conference on Advances in Computer Engineering and Applications },
issue_date = { March 2014 },
volume = { ICACEA },
number = { 5 },
month = { March },
year = { 2014 },
issn = 0975-8887,
pages = { 16-21 },
numpages = 6,
url = { /proceedings/icacea/number5/15642-1455/ },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Proceeding Article
%1 International Conference on Advances in Computer Engineering and Applications
%A Charu Sharma
%A Pankaj Agrawal
%A Preeti Gupta
%T Multiple Sequence Alignments with Parallel Computing
%J International Conference on Advances in Computer Engineering and Applications
%@ 0975-8887
%V ICACEA
%N 5
%P 16-21
%D 2014
%I International Journal of Computer Applications
Abstract

The growth of bioinformatics and computational biology industry, multiple sequence alignment (MSA) applications have become an important emerging workload. In spite of the large amount of recent attention given to the MSA software design, there has been little quantitative understanding of the performance of such applications on modern microprocessors and systems. In this paper we try to analyze performance and characteristics of MSA software from the perspective of multicore machines. We use several popular MSA programs employing a wide variety of alignment approaches. The basic workload characteristics and the efficiencies of various multicore machines features are examined . In order to mapping parallelism in multicore machines we try to explore different parallel programming approaches using threads and MPI

References
  1. J. D. Thompson, J. e. Thierry, O. Poch. (2003). RASCAL: rapid scanning and correction of multiple sequence alignments, Bioinformatics, Vol. 19, No. 9.
  2. V Amouda et. al. / International Journal of Engineering Science and Technology Vol. 2(11), 2010, 6361-6370.
  3. Thompson JD, Poch O. (2006). Multiple sequence alignment as a workbench for molecular systems biology,Curr Bioinformatics , 1:95-104.
  4. Boukerche A, Demelo A, Ayalarincon M, Walter M. (2007). Parallel strategies for the local biological sequence alignment in a cluster of workstations, J Parallel Distrib Comput , 67:170-185.
  5. Essoussi N, Boujenfa K, Limam M. (2008). A comparison of MSA tools. Bioinformation , 2:452-455.
  6. Kleinjung J, Douglas N, Heringa J. (2002). Parallelized multiple alignment,Bioinformatics , 18:1270-1271.
  7. Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B. (2004). DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics 2004, 5:128.
  8. Li K-B. (2003). ClustalW-MPI: ClustalW analysis using distributed and parallel computing, Bioinformatics , 19:1585-1586.
  9. Mikhailov D, Cofer H, Gomperts R. (2001). Performance optimization of Clustal W: parallel Clustal W, HT Clustal, and Multiclustals. In White papers. Silicon Graphics, Mountain View, CA.
  10. Zafalon,F. D. Geraldo. Et al. (2013). "Improvements in the score matrix calculation method using parallel score estimating algorithm", Journal of Biophysical Chemistry, Vol. 4,No. 2, 47-51.
  11. Zhu, X. Li, K. et al. (2011). "A Data Parallel Strategy for Aligning Multiple Biological Sequences on Homogeneous Multiprocessor Platform", Sixth Annual ChinaGrid Conference.
  12. Agarwal,P. Rizvi,S. A. M. (2009). "Solving sequence Alignment Problems using Pipeline Approach",BIJIT-BVICAM's International Journal of Information Technology
  13. Saeed, F. et al. (2009). "A Domain Decomposition Strategy for Alignment of Multiple Biological Sequences on Multiprocessor Platforms", J. Parallel Distrib. Comput.
  14. Trelles O. (2001). "On the parallelisation of bioinformatics applications", Brief Bioinform, 2:181-194.
  15. Naveed ,T. Siddiqui, I. S. (2005). "Parallel Needleman-Wunsch Algorithm for Grid", Biogridpaper.
  16. C. Notredame, D. G. Higgins, and J. Heringa. (2000). T-COFFEE: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. , 392:205–217.
  17. C. Notredame, L. Holm, and D. G. Higgin. (1998) COFFEE: An objective function for multiple sequence alignment. Bioinformatics, 14(5):407–422.
  18. J. D. Thompson, D. G. Higgins, and T. J. Gibson. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research,22(22):4673–4680.
  19. C. Notredame and D. G. Higgins. (1996). SAGA: Sequence alignment by genetic algorithm, Nucleic Acids Research, 24(8):1515–1524.
  20. Robert C. Edgar. (2004). " MUSCLE: multiple sequence alignment with high accuracy and high throughput", Journal,Nucleic Acid Research, Vol. 32(5).
  21. J. Blazewicz et al. (2013) "G-MSA — A GPU-based, fast and accurate algorithm for multiple sequence alignment", J. Parallel Distrib. Comput. 73: 32–41.
  22. ]F. J. Esteban et al. (2013). "Direct approaches to exploit many-core architecture in bioinformatics", Future Generation Computer Systems Vol. 29:15–26.
  23. Rezaei. S et al. (2006). "DIVIDE-AND-CONQUER ALGORITHM FOR CLUSTALW-MPI",IEEE CCECE/CCGEI, Ottawa, May 2006.
  24. Xiangyuan Zhu. Et al. (2013) "A data parallel strategy for aligning multiple biological sequences on multi-core computers", Computers in Biology and Medicine 43: 350–361.
  25. Dohi. K, K. Benkrid,C. Ling et al. (2010). "Highly Efficient Mapping of the Smith-Waterman Algorithm on CUDA-compatible GPUs" IEEE,ASAP.
  26. Thompson,J. D. , Higgins,D. G. and Gibson,T. J. (1994). "ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice," Nucleic Acids Research, vol. 22, pp. 4673–4680.
  27. O. Miquel, G. Fernando, N. Cedric, C. Fernando, Exploiting parallelism on progressive alignment methods, J. Supercomput. (2009) 79–87.
  28. B. Azzedine, C. Alba, A. -R. Mauricio, E. Maria, Parallel strategies for the local biological sequence alignment in a cluster of workstations, J. Parallel Distrib. Comput. 67 (2007) 170–185.
  29. K. Taecho, j. Hyun, Clustalxeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment, BMC Bioinformatics 11 (2010) 467. [
  30. H. M. Wong, V. Bharadwaj, Aligning biological sequences on distributed bus networks: a divisible load scheduling approach, IEEE Trans. Inf. Technol. Biomed. 9 (4) (2005) 489–501.
  31. V. Bharadwaj, H. M. Wong, Handling biological sequence alignments on networked computing systems: a divide-and-conquer approach, J. Parallel Distrib. Comput. 69 (2009) 854–865.
  33. H. P. L. Diana, V. Bharadwaj, A. B. David, On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multi- processor architectures, J. Parallel Distrib. Comput. 67 (2007) 1007–1017.
  34. D. P. Tommaso, M. Orobitg, F. Guirado, F. Cores, T. Espinosa, C. Notredame, Cloud-coffee: implementation of a parallel consistency-based multiple align- ment algorithm in the t-coffee package and its benchmarking on the amazon elastic-cloud, Bioinformatics 26 (15) (2010) 1903–1904.
  35. H. F. B. Vicente, L. M. David, P. Sylvain, S. Johannes, Parallel geometric algo- rithms for multi-core computers, Comput. Geometry 43 (2010) 663–677.
  36. L. Kuo-Bin, CLUSTALW-MPI: CLUSTALW analysis using distributed and parallel computing, Bioinformatics 19 (12) (2003) 1585–1586.
  37. Z. Jaroslaw, Y. Xiao, R. Adrain, A. Srinivas, Parallel-tcoffee: a parallel multiple sequence aligner, in: Proc. ISCA PDCS, 2007, pp. 248–253.
  38. S. Fahad, K. Ashfaq, A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms, J. Parallel Distrib. Comput. 69 (2009) 666–677.
  39. K. Kazutaka, T. Hiroyuki, Parallelization of the MAFFT multiple sequence alignment program, Bioinformatics 26 (15) (2010) 1899–1900.
Index Terms

Computer Science
Information Sciences

Keywords

Multiple Sequence Alignment Parallelism Multicore Machines Parallel Strategies.