Computing similarity between RNA structures
Theoretical Computer Science
The longest common subsequence problem for sequences with nested arc annotations
Journal of Computer and System Sciences - Computational biology 2002
Pattern Matching for Arc-Annotated Sequences
FST TCS '02 Proceedings of the 22nd Conference Kanpur on Foundations of Software Technology and Theoretical Computer Science
Algorithms and complexity for annotated sequence analysis
Algorithms and complexity for annotated sequence analysis
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
What makes the arc-preserving subsequence problem hard?
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Fast Arc-Annotated Subsequence Matching in Linear Space
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
Parameterized complexity of the arc-preserving subsequence problem
WG'10 Proceedings of the 36th international conference on Graph-theoretic concepts in computer science
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The Arc-Preserving Subsequence (APS) problem appears in the comparison of RNA structures in computational biology. Given two arc-annotated sequences of length n and m , APS asks if the shorter sequence can be obtained from the longer one by deleting certain elements along with their incident arcs. It is known that APS with pairwise nested arcs can be solved in O(mn) time. We give an algorithm running in O(m2 + n) time in the worst case, actually it is even faster in particular if the shorter sequence has many arcs. The result may serve as a building block for improved APS algorithms in the general case.