An efficient alignment algorithm for masked sequences

We consider the alignment problem where sequences may have masked regions. The bases in masked regions are either unspecified or unknown, and they will be denoted by N. We present an efficient algorithm that finds an optimal local alignment by skipping such masked regions of sequences. Our algorithm works for both the affine gap penalty model and the linear gap penalty model. The time complexity of our algorithm is O((n−T)(m−S)+vm+wn) time, where n and m are the lengths of given sequences A and B, T and S are the numbers of base N in A and B, and v and w are the numbers of masked regions in A and B, respectively.