DNA Physical Mapping on a Reconfigurable Platform

  • Adriano Idalgo
  • Nahri Moreano
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4943)


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.


Consecutive ones problem Reconfigurable architectures Software/hardware partitioning 


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  1. 1.
    Bondalapati, K., Prasanna, V.K.: Reconfigurable Computing Systems. Proceedings of the IEEE 90(7), 1201–1217 (2002)CrossRefGoogle Scholar
  2. 2.
    Setubal, J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company (1997)Google Scholar
  3. 3.
    Fulkerson, D., Gross, O.: Incidence Matrices and Interval Graphs. Pacific Journal of Mathematics 15(3), 835–855 (1965)zbMATHMathSciNetGoogle Scholar
  4. 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. 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. 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. 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. 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. 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. 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. 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)zbMATHMathSciNetGoogle Scholar
  12. 12.
    Xilinx: Xilinx Multimedia Board (2005),
  13. 13.
    NCBI - National Center for Biotechnology Information: NCBI (2007),

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Adriano Idalgo
    • 1
  • Nahri Moreano
    • 1
  1. 1.Department of ComputingFederal University of Mato Grosso do SulBrazil

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