The Longest Common Subsequence Problem for Arc-Annotated Sequences
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Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. Recently, the longest arc-preserving common subsequence problem has been introduced in [,] as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures and present some new algorithmic and complexity results on the longest arc-preserving common subsequence problem. Some of our results answer an open question in [,] and some others improve the hardness results in [,].
KeywordsSequence annotation longest common subsequence approximation algorithm maximum independent set MAX SNP-hard dynamic programming
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