Data structures and algorithms for approximate string matching
Journal of Complexity
On the set LCS and set-set LCS problems
Journal of Algorithms
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Sequence alignment with tandem duplication
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
The String-to-String Correction Problem
Journal of the ACM (JACM)
Parametric Combinatorial Computing and a Problem of Program Module Distribution
Journal of the ACM (JACM)
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
GapsMis: flexible sequence alignment with a bounded number of gaps
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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In this paper we consider the problem of sequence alignment with quality scores. DNA sequences produced by a base-calling program (as part of sequencing) have quality scores which represent the confidence level for individual bases. However, previous sequence alignment algorithms do not consider such quality scores. To solve sequence alignment with quality scores, we first consider a more general problem where the input is weighted sequences which are sequences with probabilities that characters occur in each position. We propose a meaningful measure of an alignment of two weighted sequences and show that an optimal alignment in this measure can be found by dynamic programming. Sequence alignment with quality scores can be solved as a special case of the weighted sequence alignment problem.