Checking Pedigree Consistency with PCS

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.