Skip to main content
SpringerLink
Log in

DNA Physical Mapping on a Reconfigurable Platform

  • Conference paper
Reconfigurable Computing: Architectures, Tools and Applications (ARC 2008)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4943))

Included in the following conference series:

  • 967 Accesses

Abstract

Reconfigurable architectures enable the hardware function to be implemented by the user and, due to its characteristics, have been used in many areas, including Bioinformatics. One application of Bioinformatics is the consecutive ones problem, which consists in finding a permutation of columns in a binary matrix, in such a way that all the ones in each row are consecutive. This matrix represents information about DNA fragments and probes, which allow the determination of the order of the nitrogenated bases that form the original DNA.

This work proposes a hybrid software/hardware system for solving the consecutive ones problem. Since this problem processes large volumes of data, the goal is to reduce its execution time, compared to a SW algorithm. We present and analyze several implementations, in the reconfigurable hardware, of sections of this algorithm, using a Virtex-II FPGA. Experiments performed using real chromosomes produced speedups of up to 29.62 and show potential for further optimizations exploiting dynamic reconfiguration.

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. Bondalapati, K., Prasanna, V.K.: Reconfigurable Computing Systems. Proceedings of the IEEE 90(7), 1201–1217 (2002)

    Article  Google Scholar 

  2. Setubal, J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company (1997)

    Google Scholar 

  3. Fulkerson, D., Gross, O.: Incidence Matrices and Interval Graphs. Pacific Journal of Mathematics 15(3), 835–855 (1965)

    MATH  MathSciNet  Google Scholar 

  4. Jacobi, R.P., Rincón, M.A., Carvalho, L.G., Llanos, C.H., Hartenstein, R.W.: Reconfigurable Systems for Sequence Alignment and for General Dynamic Programming. In: Proceedings of the Brazilian Workshop on Bioinformatics, pp. 25–32 (2004)

    Google Scholar 

  5. Oliver, T., Schmidt, B., Maskell, D.: Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs. In: Proceedings of the International Symposium on Field-Programmable Gate Arrays, pp. 229–237 (2005)

    Google Scholar 

  6. Regester, K., Byun, J.H., Mukherjee, A., Ravindran, A.: Implementing Bioinformatics Algorithms on Nallatech-Configurable Multi-FPGA Systems. Xcell Journal Online (53), 100–103 (2005)

    Google Scholar 

  7. Meng, X., Chaudhary, V.: An Adaptive Data Prefetching Scheme for Biosequence Database Search on Reconfigurable Platforms. In: Proceedings of the ACM Symposium on Applied Computing, pp. 140–141 (2007)

    Google Scholar 

  8. Mak, T.S.T., Lam, K.P.: Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA. In: Proceedings of the IEEE Computational Systems Bioinformatics Conference, pp. 512–514 (2004)

    Google Scholar 

  9. Krishnamurthy, P., Buhler, J., Chamberlain, R.D., Franklin, M.A., Gyang, K., Jacob, A., Lancaster, J.: Biosequence Similarity Search on the Mercury System. In: Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors, pp. 365–375 (2004)

    Google Scholar 

  10. Hsu, W.L.: A Simple Test for the Consecutive Ones Property. In: Ibaraki, T., Iwama, K., Yamashita, M., Inagaki, Y., Nishizeki, T. (eds.) ISAAC 1992. LNCS, vol. 650, pp. 459–468. Springer, Heidelberg (1992)

    Google Scholar 

  11. Booth, K.S., Lueker, G.S.: Testing for the Consecutive Ones Property, Interval Graphs, and Graph Planarity Using PQ-tree Algorithms. Journal of Computer and System Sciences 13(3), 335–379 (1976)

    MATH  MathSciNet  Google Scholar 

  12. Xilinx: Xilinx Multimedia Board (2005), http://www.xilinx.com

  13. NCBI - National Center for Biotechnology Information: NCBI (2007), http://www.ncbi.nlm.nih.gov/

Download references

Author information

Authors and Affiliations

  1. Department of Computing, Federal University of Mato Grosso do Sul, Brazil

    Adriano Idalgo & Nahri Moreano

Authors
  1. Adriano Idalgo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nahri Moreano
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Roger Woods Katherine Compton Christos Bouganis Pedro C. Diniz

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Idalgo, A., Moreano, N. (2008). DNA Physical Mapping on a Reconfigurable Platform. In: Woods, R., Compton, K., Bouganis, C., Diniz, P.C. (eds) Reconfigurable Computing: Architectures, Tools and Applications. ARC 2008. Lecture Notes in Computer Science, vol 4943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78610-8_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-78610-8_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-78609-2

  • Online ISBN: 978-3-540-78610-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation