Pseudo-Boolean Multiple Sequence Alignment

Multiple sequence alignment is a central problem in Bioinformatics and a challenging one for optimisation algorithms. An established integer programming approach is to apply branch-and-cut to a graph-theoretical model. The models are exponentially large but are represented intensionally, and violated constraints can be located in polynomial time. This report describes a new integer program formulation that generates polynomial-sized models small enough to be passed to generic solvers. It is a hybrid formulation relating the sparse alignment graph with a compact encoding of the alignment matrix via channelling constraints. Alignments obtained with a pseudo-Boolean local search algorithm are competitive with those of state-of-the-art algorithms. Execution times are much longer, but in future work we aim to develop a more efficient specialised algorithm.