We apologize for a recent technical issue with our email system, which temporarily affected account activations. Accounts have now been activated. Authors may proceed with paper submissions. PhDFocusTM
CFP last date
20 December 2024
Call for Paper
January Edition
IJCA solicits high quality original research papers for the upcoming January edition of the journal. The last date of research paper submission is 20 December 2024

Submit your paper
Know more
The week's pick
Responsive image
Improved Shuffled Frog Leaping Algorithm with Self-Adaptive Shuffling for Fuzzy Logic PD+G Controller Optimization in Robotic Manipulators

Duc Hoang Nguyen
Random Articles
Reseach Article

Parallel Two Master Method to Improve BLAST Algorithm’s Performance

by Muralidhara B L
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 63 - Number 1
Year of Publication: 2013
Authors: Muralidhara B L
10.5120/10428-5097

Muralidhara B L . Parallel Two Master Method to Improve BLAST Algorithm’s Performance. International Journal of Computer Applications. 63, 1 ( February 2013), 8-14. DOI=10.5120/10428-5097

@article{ 10.5120/10428-5097,
author = { Muralidhara B L },
title = { Parallel Two Master Method to Improve BLAST Algorithm’s Performance },
journal = { International Journal of Computer Applications },
issue_date = { February 2013 },
volume = { 63 },
number = { 1 },
month = { February },
year = { 2013 },
issn = { 0975-8887 },
pages = { 8-14 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume63/number1/10428-5097/ },
doi = { 10.5120/10428-5097 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T21:12:59.914024+05:30
%A Muralidhara B L
%T Parallel Two Master Method to Improve BLAST Algorithm’s Performance
%J International Journal of Computer Applications
%@ 0975-8887
%V 63
%N 1
%P 8-14
%D 2013
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The BLAST heuristic algorithm is one of the widely used algorithms for finding similar sequences in sequence databases. The paper acquires importance as traditional approaches to sequence homology searches using BLAST have proven to be too slow to keep up with the current rate of sequence acquisition. The use of the BLAST application on a single processor has become too costly, inefficient, and time-consuming for many life science laboratories. An obvious improvement that has already been suggested is the use of database segmentation to speedup BLAST. A two master method to improve the performance of the parallel BLAST algorithm is presented here. It is found that the two master method has performed better than the single master method.

References
  1. Altschul F Stepehn, Tomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman. 1997. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research, Vol. 25, No. 17, 3389-3402.
  2. Altschul F Stephen, Ralf Bundschuh, Rolf Olsen and Terence Hwa. 2001. "The estimation of statistical parameters for local alignment score distributions". Nucleic Acids Research, Vol. 29, No. 2, pp. 351-361.
  3. Altschul F Stephen, Warren Gish, Webb Miller, Eugene W. Myers & David J. Lipman. 1990. "Basic Local Alignment Search Tool". Journal of Molecular Biology, 215, 403-410.
  4. Bjornson R. D, A. H. Sherman, S. B. Weston, N. Willard, J. Wing. 2002. "TurboBLAST: A Parallel Implementation of BLAST Built on the TruboHub". Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS'02), IEEE Computer Society.
  5. Braun R. C, K. T. Pedretti, T. L. Casavant, T. E. Scheetz, C. L. Birkett, C. A. Roberts. 2001. "Parallelization of local BLAST service on workstation clusters". Future Generation Computer Systems, Vol. 17, pp. 745-754.
  6. Darling E Aaron, Lucan Carey, Wu-dhun Feng. 2003. "The Design, Implementation, and Evaluation of mpiBLAST". ClusterWorld Conference & Expo and the 4th International Conference on Linux Clusters: The HPC Revolution 2003. LA-UR 03-2862.
  7. Delcher L Arthur, Adam Phillippy, Jane Carlton and Steven L. Salzberg. 2002. "Fast algorithms for large-scale genome alignment and comparison". Nucleic Acids Research, Vol. 30, No. 11, 2478-2483.
  8. Delcher L Arthur, Simon Kasif, Robert D. Fleischmann, Jeremy Peterson, Owen White and Steven L Salzberg. 1999. "Alignment of whole genomes". Nucleic Acids Research, Vol. 27, No. 11, 2369-2376.
  9. Feng, W. "Green Destiny + mpiBLAST = Bioinformagic". 2003. 10th International Conference on Parallel Computing: Bioinformatics Symposium, PARCO, pp. 653-660.
  10. Grant J. D, R. L. Dunbrack, F. J. Manion and M. F. Ochs. 2002. "BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster". Bioinformatics. Vol. 18 no. 5, pp. 765-766.
  11. Gropp William, Ewing Lusk, Anthony skjellum. 1999. Using MPI – Portable Parallel Programming with message-passing Interface, Second edition. London, England, Cambridge, Massachusetts: The MIT Press.
  12. Julich Anne. 2002. "Implementations of BLAST for Parallel Computers". CABIOS. Vol. 11, no. 1, pp. 3-6.
  13. Kent James. W. 2002. "BLAT – The BLAST-Like Alignment Tool". Genome Research, Vol. 12, pp. 656-664.
  14. Kurtz Atefan and Chris Schleiermacher. 1999. "REPuter: fast computation on maximal repeats in complete genomes". Bioinformatics, Vol. 15, no. 5, 426-427.
  15. Ma Bin, Joh Tromp and Ming Li. "Pattern Hunter: faster and more sensitive homology search". 2002. Bioinformatics, Vol. 18, no. 3, pp. 440-445.
  16. Mathog. R David. 2003. "Parallel BLAST on split databases". Bioinformatics, Vol. 19, no. 14, 1865-1866.
  17. Needleman Saul B & Christian D. Wunsch. 1970. "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins". Journal of Molecular Biology, 48, 443-453.
  18. Person W R and Miller W. 1992. "Dynamic Programming algorithm for biological sequence comparison". Methods Enzymol, Vol. 210, pp. 575-601.
  19. Smith T. F, & M. S. Waterman. 1981. "Identification of Common Molecular Sequences". Journal of Molecular Biology, 147, 195-197.
Index Terms

Computer Science
Information Sciences

Keywords

Sequence alignment BLAST Database segment Query segment Efficiency Speedup

Powered by PhDFocusTM