Algorithms for Local Alignment with Length Constraints
نویسندگان
چکیده
The local sequence alignment problem is the detection of similar subsequences in two given sequences of lengths n m. Unfortunately the common notion of local alignment suuers from some well-known anomalies which result from not taking into account the lengths of the aligned subsequences. We introduce the length restricted local alignment problem which includes as a constraint an upper limit T on the length of one of the subsequences to be aligned. We propose an eecient approximation algorithm using which we can nd a solution satisfying the length bound, and whose score is within diierence of the optimum score for any given positive integer in time O(nmT=) using O(mT=) space. We also introduce the cyclic local alignment problem and show how our idea can be applied to this case as well. This is a dual approach to the well-known cyclic edit distance problem.
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