Communications of the ACM
The CLP( R ) language and system
ACM Transactions on Programming Languages and Systems (TOPLAS)
Parametric optimization of sequence alignment
SODA '92 Proceedings of the third annual ACM-SIAM symposium on Discrete algorithms
The String-to-String Correction Problem
Journal of the ACM (JACM)
Mathematical Methods for DNA Sequences
Mathematical Methods for DNA Sequences
Applications in Constraint Logic Programming with Strings
PPCP '94 Proceedings of the Second International Workshop on Principles and Practice of Constraint Programming
A constraint solver for flexible protein models
Journal of Artificial Intelligence Research
| Hi-index | 0.00 |
Approximate matching techniques based on string alignment are important tools for investigating similarities between strings, such as those representing DNA and protein sequences. We propose a constraint based approach for parametric sequence alignment which allows for more general string alignment queries where the alignment cost can itself be parameterized as a query with some initial constraints. Thus, the costs need not be fixed in a parametric alignment query unlike the case in normal alignment. The basic dynamic programming string edit distance algorithm is generalized to a naive algorithm which uses inequalities to represent the alignment score. The naive algorithm is rather costly and the remainder of the paper develops an improvement which prunes alternatives where it can and approximates the alternatives otherwise. This reduces the number of inequalities significantly and strengthens the constraint representation with equalities. We present some preliminary results using parametric alignment on some general alignment queries.