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)

Abstract

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.

Keywords

Boolean satisfiability SAT Pedigree Consistency checking bioinformatics genetics computational biology 

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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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