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What SAT can do for BioInformatics ? Compact Models and Efficient Algorithms Haplotype Inference • SAT and SAT extensions provide compact models and efficient algorithms • Problem Description: Given a set G of n genotypes, find a set H of 2n haplotypes (not necessarily distinct), such that for each genotype gi in G there is at least one pair of haplotypes (hj,hk), with hk and hj in H such that the pair (hj,hk) explains gi • Efficient solvers are available for both SAT and SAT extensions • Technology used: SAT and Pseudo Boolean Optimization • SAT is a well known problem and a area of intensive research • Reference: J. Marques-Silva and I. Lynce, AAAI 06 Checking Pedigree Consistency SAT & SAT Extensions • Problem Description: Given a pedigree check if it is consistent with the Mendelian laws of inheritance, i.e., check if every individual inherits exactly one allele from each of its parents • Technology used: SAT by translation into CNF • Reference: P. Manolios, M. Galceran Oms and S. Oliva Valls, TACAS 07 Genome Rearrangement Distance • Problem Description: Compute the exact genomic distance between two genomes in the presence of duplications, namely, determining the maximum number of common intervals between the genomes • Technology used: Pseudo Boolean Optimization • Reference: S.Angibaud, G.Fertin, I.Rusu and S.Vialette, RECOMB-CG 06 Protein Folding • Problem Description: Given a sequence of amino acids of a protein, determine the structure to which the protein folds • Technology used: Pseudo Boolean Optimization (PBO) • Current stage: currently a first attempt to directly translate the HP Lattice Model to PBO has been done Other…? • Besides SAT itself, other extensions of SAT might be used to solve problems of BioInformatics: o Pseudo Boolean Optimization o Satisfiability Module Theories o SAT Enumeration o Counting SAT o Quantified Boolean Formulas o… • Given the sequence “PHPPHPHP” the energy of the conformation in the right is -2 • Expected future steps: Inclusion of lower bounds that are able to efficiently reduce the search space Introduction of techniques to break and remove symmetries António Morgado - [email protected] Dr. João Marques Silva - [email protected] This work is being supported by Microsoft Research through its European PhD Scholarship Programme