This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computation time and O(M+N) space, where F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.
All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Environmental Science(all)
- Agricultural and Biological Sciences(all)
- Computational Theory and Mathematics