Checking Pedigree Consistency with PCS

  • Panagiotis Manolios
  • Marc Galceran Oms
  • Sergi Oliva Valls
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4424)


Many important problems in bioinformatics and genetics require analyses that are NP-complete. For example, one of the basic problems facing researchers that analyze pedigrees—data that represents relationships and genetic traits of a set of individuals—is evaluating whether they are consistent with the Mendelian laws of inheritance. This problem is NP-complete and several specialized algorithms have been devised to solve the types of problems occurring in practice efficiently. In this paper, we present PCS, a tool based on Boolean Satisfiability (SAT) that is orders of magnitude faster than existing algorithms, and more general. In fact, PCS can solve real pedigree checking problems that cannot be solved with any other existing tool.


Boolean satisfiability SAT Pedigree Consistency checking bioinformatics genetics computational biology 


  1. 1.
    Aceto, L., et al.: The complexity of checking consistency of pedigree information and related problems. In: Blundo, C., Laneve, C. (eds.) ICTCS 2003. LNCS, vol. 2841, pp. 174–187. Springer, Heidelberg (2003)Google Scholar
  2. 2.
    de Givry, S., et al.: Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques. In: ICLP-05 workshop on Constraint Based Methods for Bioinformatics, Sitges, Spain (2005)Google Scholar
  3. 3.
    Lange, K., Goradia, T.: An algorithm for automatic genotype elimination. American Journal of Human Genetics 40(3), 250–256 (1987)Google Scholar
  4. 4.
    Manolios, P., Oms, M.G., Valls, S.O.: PCS: Pedigree Checking with SAT (2007), Available from
  5. 5.
    Manolios, P., Srinivasan, S.K., Vroon, D.: Automatic memory reductions for RTL-level verification. In: ACM-IEEE International Conference on Computer Aided Design (ICCAD 2006) (November 2006)Google Scholar
  6. 6.
    Manolios, P., Srinivasan, S.K., Vroon, D.: BAT: The Bit-level Analysis Tool (2006), Available from
  7. 7.
    Moskewicz, M.W., et al.: Chaff: Engineering an efficient SAT solver. In: Design Automation Conference (DAC’01), pp. 530–535 (2001)Google Scholar
  8. 8.
    O’Connell, J.R., Weeks, D.E.: Pedcheck: A program for identification of genotype incompatibilities in linkage analysis. American Journal of Human Genetics 63(1), 259–266 (1998)CrossRefGoogle Scholar
  9. 9.
    O’Connell, J.R., Weeks, D.E.: An optimal algorithm for automatic genotype elimination. American Journal of Human Genetics 65(6), 1733–1740 (1999)CrossRefGoogle Scholar
  10. 10.
    Sobel, E., Papp, J.C., Lange, K.: Detection and integration of genotyping errors in statistical genetics. American Journal of Human Genetics 70, 496–508 (2002)CrossRefGoogle Scholar
  11. 11.
    Zhang, L., Malik, S.: Validating SAT solvers using an independent resolution-based checker: Practical implementations and other applications. In: Proceedings of the Design and Test in Europe Conference, March 2003, pp. 10880–10885 (2003)Google Scholar

Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Panagiotis Manolios
    • 1
  • Marc Galceran Oms
    • 1
  • Sergi Oliva Valls
    • 1
  1. 1.College of Computing, Georgia Institute of Technology, AtlantaGeorgia 30332-0280 USA

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