Table of Contents Author Guidelines Submit a Manuscript
International Journal of Reconfigurable Computing
Volume 2012, Article ID 201378, 19 pages
http://dx.doi.org/10.1155/2012/201378
Research Article

A Protein Sequence Analysis Hardware Accelerator Based on Divergences

1Electrical Engineering Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
2School of Computing, Federal University of Mato Grosso do Sul, Campo Grande, MS 79070-900, Brazil
3Computer Science Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
4UnB Gama School, University of Brasilia, Gama, DF 72405-610, Brazil

Received 27 September 2011; Accepted 26 December 2011

Academic Editor: Khaled Benkrid

Copyright © 2012 Juan Fernando Eusse et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. The Universal Protein Resource—UniProt, June 2009, http://www.uniprot.org/.
  2. Sanger's Institute PFAM Protein Sequence Database, May 2009, http://pfam.sanger.ac.uk/.
  3. A. C. Jacob, J. M. Lancaster, J. D. Buhler, and R. D. Chamberlain, “Preliminary results in accelerating profile HMM search on FPGAs,” in Proceedings of the 21st International Parallel and Distributed Processing Symposium, (IPDPS '07), Long Beach, Calif, USA, March 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. “HMMER: biosequence analysis using profile hidden Markov models,” 2006, http://hmmer.janelia.org/.
  5. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, New York, NY, USA, 2008.
  6. R. Darole, J. P. Walters, and V. Chaudhary, “Improving MPI-HMMER’s scalability with parallel I/O,” Tech. Rep. 2008-11, Department of Computer Science and Engineering, University of Buffalo, Buffalo, NY, USA, 2008. View at Google Scholar
  7. G. Chukkapalli, C. Guda, and S. Subramaniam, “SledgeHMMER: a web server for batch searching the Pfam database,” Nucleic Acids Research, vol. 32, supplement 2, pp. W542–W544, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. “HMMER on the sun grid project,” July 2009, http://www.psc.edu/general/software/packages/hmmer/.
  9. D. R. Horn, M. Houston, and P. Hanrahan, “ClawHMMER: a streaming HMMer-search implementation,” in Proceedings of the ACM/IEEE Supercomputing Conference, (SC '05), November 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. GPU-HMMER, July 2009, http://www.mpihmmer.org/userguideGPUHMMER.htm.
  11. R. P. Maddimsetty, J. Buhler, R. D. Chamberlain, M. A. Franklin, and B. Harris, “Accelerator design for protein sequence HMM search,” in Proceedings of the 20th Annual International Conference on Supercomputing (ICS '06), pp. 288–296, New York, NY, USA, July 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. “BLAST: Basic Local Alignment Search Tool,” September 2009, http://blast.ncbi.nlm.nih.gov/.
  13. K. Benkrid, P. Velentzas, and S. Kasap, “A high performance reconfigurable core for motif searching using profile HMM,” in Procedings of the NASA/ESA Conference on Adaptive Hardware and Systems (AHS '08), pp. 285–292, Noordwijk, The Netherlands, June 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. T. F. Oliver, B. Schmidt, Y. Jakop, and D. L. Maskell, “High speed biological sequence analysis with hidden Markov models on reconfigurable platforms,” IEEE Transactions on Information Technology in Biomedicine, vol. 13, no. 5, pp. 740–746, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. J. P. Walters, X. Meng, V. Chaudhary et al., “MPI-HMMER-boost: distributed FPGA acceleration,” Journal of VLSI Signal Processing Systems, vol. 48, no. 3, pp. 223–238, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Derrien and P. Quinton, “Parallelizing HMMER for hardware acceleration on FPGAs,” in Proceedings of the International Conference on Application-specific Systems, Architectures and Processors (ASAP '07), pp. 10–17, Montreal, Canada, July 2007.
  17. L. Hunter, Artificial Intelligence and Molecular Biology, MIT Press, 1st edition, 1993.
  18. D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997.
  19. L. R. Rabiner, “A tutorial on hidden Markov models and selected applications in speech recognition,” Proceedings of the IEEE, vol. 77, no. 2, pp. 257–286, 1989. View at Publisher · View at Google Scholar · View at Scopus
  20. Y. Sun, P. Li, G. Gu et al., “HMMer acceleration using systolic array based reconfigurable architecture,” in Proceedings of the ACM/SIGDA International Symposium on Field Programmable Gate Arrays (FPGA '09), p. 282, New York, NY, USA, May 2009. View at Publisher · View at Google Scholar
  21. T. Takagi and T. Maruyama, “Accelerating hmmer search using FPGA,” in Proceedings of the19th International Conference on Field Programmable Logic and Applications (FPL '09), pp. 332–337, Prague Czech Republic, September 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. R. B. Batista, A. Boukerche, and A. C. M. A. de Melo, “A parallel strategy for biological sequence alignment in restricted memory space,” Journal of Parallel and Distributed Computing, vol. 68, no. 4, pp. 548–561, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. XtremeData Inc., July 2009, http://www.xtremedata.com/.