Abstract
Multiple sequence alignment is a central problem in Bioinformatics. A known integer programming approach is to apply branch-and-cut to exponentially large graph-theoretic models. This paper describes a new integer program formulation that generates models small enough to be passed to generic solvers. The formulation is a hybrid relating the sparse alignment graph with a compact encoding of the alignment matrix via channelling constraints. Alignments obtained with a SAT-based local search algorithm are competitive with those of state-of-the-art algorithms, though execution times are much longer.
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Prestwich, S., Higgins, D., O’Sullivan, O. (2003). A SAT-Based Approach to Multiple Sequence Alignment. In: Rossi, F. (eds) Principles and Practice of Constraint Programming – CP 2003. CP 2003. Lecture Notes in Computer Science, vol 2833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45193-8_83
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DOI: https://doi.org/10.1007/978-3-540-45193-8_83
Publisher Name: Springer, Berlin, Heidelberg
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