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Bit-Parallel Algorithm for the Constrained Longest Common Subsequence Problem

Deorowicz S.

Fundamenta Informaticae

2010

Vol. 99, nr 4

409-433

The problem of finding a constrained longest common subsequence (CLCS) for the sequences A and B with respect to the sequence P was introduced recently. Its goal is to find a longest subsequence C of A and B such that P is a subsequence of C. Most of the algorithms solving the CLCS problem are based on dynamic programming. Bit-parallelism is a technique of using single bits in a machine word for concurrent computation. We propose the first bit-parallel algorithm computing a CLCS and/or its length which outperforms the other known algorithms in terms of speed.