Skip to main content
SpringerLink
Log in

Grid-Enabled BLASTZ: Application to Comparative Genomics

  • Published:
The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology Aims and scope Submit manuscript

Abstract

BLASTZ is a sequence alignment tool designed mainly for aligning neutrally evolved bio-sequences and has been the choice for aligning noncoding sequences. However, its running time is impractical for high throughput alignment of long sequences, for example, for the alignment of human and mouse genomes. In order to improve the performance and efficiency for alignment at genome scale, BLASTZ was implemented using the GLOBUS toolkit on a computing grid. A dynamic load balancing technique was introduced to achieve enhanced performance on a grid which consists of sources of heterogeneous characteristics, such as resources of different computational powers. The robustness of the implementation to disturbances due to other processes on the grid is demonstrated.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic Local Alignment Search Tool,” J. Mol. Biol., vol. 215, 1990, 403–410.

    Google Scholar 

  2. S. F. Altschul, T. L. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, “Gapped BLAST and PSI-BLAST—A New Generation of Protein Database Search Programs,” Nucleic Acids Res., vol. 25, 1997, 3389–3402.

    Article  Google Scholar 

  3. C. X. Chen and B. Schmidt, “An Adaptive Grid Implementation of DNA Sequence Alignment,” Future Generation Computer Systems—The International Journal of Grid Computing: Theory, Methods and Applications, vol. 21, no. 7, 2005, pp. 988–1003.

    Google Scholar 

  4. C. X. Chen and B. Schmidt, “Constructing Large Suffix Trees on a Computational Grid,” Journal of Parallel Distributed Computing, in press, doi: 10.1016/j.jpdc.2006.08.004.

  5. E. T. Dermitzakis, A. Reymond, R. Lyle, N. Scamuffa, C. Ucla, S. Deutsch, etc., “Numerous Potentially Functional but Non-genic Conserved Sequences on Human Chromosome 21,” Nature, vol. 420, 2002.

  6. B. Giardine, L. Elnitski, C. Riemer, L. Makalowska, S. Schwartz, W. Miller, “GALA, a Database for Genomic Sequence Alignments and Annotations,” Genome Res., vol. 13, 2003, 732–741.

    Article  Google Scholar 

  7. Y. Gitton, N. Dahmane, S. Baik, A. R. i Altaba, L. Neidhardt, M. Scholze, B. G. Herrmann, P. Kahlemk, A. Benkahlak, S. Schrinnerk, R. Yildirimmank, R. Herwigk, H. Lehrachk, and M.-L. Yaspok, “A Gene Expression Map of Human Chromosome 21 Orthologues in the Mouse,” Nature, vol. 420, 2002.

  8. A. Reymond, V. Marigo, M. B. Yaylaoglu, A. Leoni, C. Ucla, N. Scamuffa, C. Caccioppoli, E. T. Dermitzakis, R. Lyle, S. Banfi, G. Eichele, S. E. Antonarakis, and A. Ballabio, “Human Chromosome 21 Gene Expression Atlas in the Mouse,” Nature, 420, 2002.

  9. S. Karlin and S. F. Altschul, “Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes,” Proc. Natl. Acad. Sci., vol. 87, 1990, 2264–2268.

    Article  MATH  Google Scholar 

  10. S. Karlin and S. F. Altschul, “Applications and Statistics for Multiple High-Scoring Segments in Molecular Sequences,” Proc. Natl. Acad. Sci., vol. 90, 1993, 5873–5877.

    Article  Google Scholar 

  11. I. Foster, C. Kesselman, and M. Kaufmann, “The Grid 2: Blueprint for a New Computing Infrastructure,” 2003.

  12. A. Krishnan, “GridBLAST: a Globus-Based High-Throughput Implementation of BLAST in a Grid Computing Framework,” Concurrency and Computation: Practice and Experience, vol. 17, no. 13, 2005, pp. 1607–1623.

    Article  Google Scholar 

  13. R. C. Hardison “Comparative Genomics,” PLoS Biol., vol. 1, no. 2, 2003, pp. e58.

    Article  Google Scholar 

  14. D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, and M. B. Eisen, “Benchmarking Tools for the Alignment of Functional Noncoding DNA,” BMC Bioinformatics, 2004.

  15. B. Schmidt, C. X. Chen, W. G. Liu, “Hierarchical Grid Computing for High Performance Bioinformatics”, in Grids for Bioinformatics and Computational Biology, Wiley, to appear in 2007.

  16. S. Schwartz, W. J. Kent, A. Smit, Z. Zhang, R. Baertsch, R. C. Hardison, D. Haussler, and W. Miller, “Human–mouse Alignments with BLASTZ,” Genome Res., vol. 13, 2003, pp. 103–107.

    Article  Google Scholar 

  17. C. A. Stewart, D. Hart, D. K. Berry, G. J. Olsen, E. A. Wernert, and F. W. ischer, “Parallel Implementation and Performance of fastDNAml: A Program for Maximum Likelihood Phylogenetic Inference,” SC2001. Denver, CO, USA. 2001.

  18. O. Trelles, “On the Parallelisation of Bioinformatics Applications,” Brief. Bioinform., vol. 2, no. 2, 2001, 181–194.

    Article  Google Scholar 

  19. W. R. Zhu, Y. W. Niu, J. Z. Lu, C. Shen, and G. R. Gao, “A Cluster-Based Solution for High Performance Hmmpfam Using EARTH Execution Model,” Cluster 2003, 2003.

  20. BLAST Manual: http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml

  21. BLASTZ Alignment Program: http://www.bx.psu.edu/miller\_lab/

  22. Conserved Non-coding Databases: http://pipeline.lbl.gov/cgi-bin/cnc

  23. Ensembl Project: http://www.ensembl.org/index.html

  24. GLOBUS Project: http://www.globus.org

  25. Master-Slave paradigm: http://charm.cs.uiuc.edu/research/masterSlave/

  26. Sun grid engine project: http://gridengine.sunsource.net/

Download references

Author information

Authors and Affiliations

  1. BioInformatics Research Center, School of Computer Engineering, Nanyang Technological University, Singapore, Singapore

    Chunxi Chen & Jagath C. Rajapakse

  2. Singapore-MIT Alliance, Singapore, Singapore

    Jagath C. Rajapakse

Authors
  1. Chunxi Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jagath C. Rajapakse
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jagath C. Rajapakse.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chen, C., Rajapakse, J.C. Grid-Enabled BLASTZ: Application to Comparative Genomics. J VLSI Sign Process Syst Sign Im 48, 301–309 (2007). https://doi.org/10.1007/s11265-007-0065-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11265-007-0065-6

Keywords

Search

Navigation