Skip to main content
SpringerLink
Log in

Distributed BLAST in a Grid Computing Context

  • Conference paper
Computational Life Sciences (CompLife 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3695))

Included in the following conference series:

Abstract

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. BRIDGES project, http://www.brc.dcs.gla.ac.uk/projects/bridges/

  2. Sinnott, R., Atkinson, M., Bayer, M., Berry, D., Dominiczak, A., Ferrier, M., Gilbert, D., Hanlon, N., Houghton, D., Hunt, E., White, D.: Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data. In: Proceedings of the UK e-Science All Hands Meeting, Nottingham, UK (2004)

    Google Scholar 

  3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. J. Mol. Biol. 215, 403–410 (1990)

    Google Scholar 

  4. EBI BLAST, http://www.ebi.ac.uk/blastall/index.html

  5. NCBI BLAST, website: http://www.ncbi.nlm.nih.gov/BLAST/

  6. Pedretti, K.T., Casavant, T.L., Braun, R.C., Scheetz, T.E., Birkett, C.L., Roberts, C.A.: Three Complementary Approaches to Parallelization of Local BLAST Service on Workstation Clusters (invited paper). In: Proceedings of the 5th International Conference on Parallel Computing Technologies, pp. 271–282 (1999)

    Google Scholar 

  7. Braun, R.C., Pedretti, K.T., Casavant, T.L., Scheetz, T.E., Birkett, C.L., Roberts, C.A.: Parallelization of local BLAST service on workstation clusters. Future Generation Computer Systems 17, 745–754 (2001)

    Article  MATH  Google Scholar 

  8. Clifford, R., Mackey, A.J.: Disperse: a simple and efficient approach to parallel database searching. Bioinformatics 16, 564–565 (2000)

    Article  Google Scholar 

  9. Mathog, D.R.: Parallel BLAST on split databases. Bioinformatics 19, 1865–1866 (2003)

    Article  Google Scholar 

  10. Darling, A.E., Carey, L., Feng, W.: The design, implementation and evaluation of mpiBLAST. In: Proceedings of ClusterWorld Conference, Expo and the 4th International Conference on Linux Clusters: The HPC Revolution (2003)

    Google Scholar 

  11. Hokamp, K., Shields, D.C., Wolfe, K.H., Caffrey, D.R.: Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics 19, 441–442 (2003)

    Article  Google Scholar 

  12. GridBlast at Keck BioCenter, University of Wisconsin, http://bioinf.ncsa.uiuc.edu/

  13. GridBlast at A-Star Bioinformatics Institute Singapore: http://www.bii.astar.edu.sg/infoscience/dcg/gridGridblast/index.asp

  14. North Carolina BioGrid, http://www.ncbiogrid.org/tech/apps.html

  15. RIKEN GridBlast, http://big.gsc.riken.jp/big/Members/fumikazu/Activity_Item.2004-02-02.0425

  16. mpiBLAST, http://mpiblast.lanl.gov/

  17. ScotGRID, http://www.scotgrid.ac.uk/

  18. OpenPBS, http://www.openpbs.org/

  19. Condor, http://www.cs.wisc.edu/condor/

  20. Globus WSRF, http://www.globus.org/wsrf/default.asp

  21. GenBank statistics, http://www.ncbi.nih.gov/Genbank/genbankstats.html

  22. OGSA Open Grid Services Architecture, http://www.gridforum.org/documents/GWD-I-E/GFD-I.030.pdf

  23. Foster, I., Kesselman, C., Tuecke, S.: The Anatomy of the Grid: Enabling Scalable Virtual Organizations. International J. Supercomputer Applications 15(3) (2001)

    Google Scholar 

  24. Globus toolkit version 2.4.3, http://www-fp.globus.org/gt2.4/

  25. Java Cog kit version 1.1, http://www-unix.globus.org/cog/java/1.1/

  26. UK National Grid Service, http://www.ngs.ac.uk/

  27. PERMIS Grid authorisation software, http://www.permis.org

  28. The U.K.: e-Science Programme, http://www.rcuk.ac.uk/escience/

  29. Globus toolkit, http://www.globus.org/toolkit/

  30. Cardiovascular Functional Genomics project, http://www.brc.dcs.gla.ac.uk/projects/cfg

  31. Scottish Bioinformatics Research Network project, http://www.nesc.ac.uk/hub/projects/sbrn

Download references

Author information

Authors and Affiliations

  1. National e-Science Centre, e-Science Hub, Kelvin Building, University of Glasgow, Glasgow, G12 8QQ

    Micha M. Bayer & Richard Sinnott

Authors
  1. Micha M. Bayer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Richard Sinnott
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Berkeley Initiative in Soft Computing (BISC), University of California at Berkeley, USA

    Michael R. Berthold

  2. Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, CB2 1EW, Cambridge, UK

    Robert C. Glen

  3. Department of Biology, University of Konstanz, Box M647, 78457, Konstanz, Germany

    Kay Diederichs

  4. Division for Simulation of Biological Systems, Center for Bioinformatics Tübingen, Eberhard Karls University Tübingen, 72076, Tübingen, Germany

    Oliver Kohlbacher

  5. ALTANA Chair for Bioinformatics and Information Mining, University of Konstanz, Germany

    Ingrid Fischer

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Bayer, M.M., Sinnott, R. (2005). Distributed BLAST in a Grid Computing Context. In: R. Berthold, M., Glen, R.C., Diederichs, K., Kohlbacher, O., Fischer, I. (eds) Computational Life Sciences. CompLife 2005. Lecture Notes in Computer Science(), vol 3695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560500_22

Download citation

  • DOI: https://doi.org/10.1007/11560500_22

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29104-6

  • Online ISBN: 978-3-540-31726-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation