A Binary Integer Programming model for computing DNA Sequence Alignment

Abstract

DNA Sequence Alignment is an important problem in computational biology and is useful for comparing genomes and finding genes, for determining evolutionary linkage of different biological sequences. Dynamic Programming Problems is discussed and applied to solve this problem. This paper is concerned with computing DNA Sequence Alignment firstly by formulating a Binary Integer Programming model to compute the string sequence in Edit Distance Problem then re-formulating this model to be suitable to compute this alignment. By this model we gave a good role for Operations Researches field to prove it's efficient to solve problems of molecule of life. The suggested model is applied to solve an example in Edit Distance Problem then used again after re-formulating it for an example in DNA Sequence Alignment Problem.