Displaying similar documents to “Faster backtracking algorithms for the generation of symmetry-invariant permutations.”

A sparse dynamic programming algorithm for alignment with non-overlapping inversions

Alair Pereira Do Lago, Ilya Muchnik, Casimir Kulikowski (2005)

RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications

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Alignment of sequences is widely used for biological sequence comparisons, and only biological events like mutations, insertions and deletions are considered. Other biological events like inversions are not automatically detected by the usual alignment algorithms, thus some alternative approaches have been tried in order to include inversions or other kinds of rearrangements. Despite many important results in the last decade, the complexity of the problem of alignment with inversions...

Sorting with a forklift.

Albert, M.H., Atkinson, M.D. (2003)

The Electronic Journal of Combinatorics [electronic only]

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A new practical linear space algorithm for the longest common subsequence problem

Heiko Goeman, Michael Clausen (2002)

Kybernetika

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This paper deals with a new practical method for solving the longest common subsequence (LCS) problem. Given two strings of lengths m and n , n ≥ m , on an alphabet of size s , we first present an algorithm which determines the length p of an LCS in O ( n s + min { m p , p ( n - p ) } ) time and O ( n s ) space. This result has been achieved before [ric94,ric95], but our algorithm is significantly faster than previous methods. We also provide a second algorithm which generates an LCS in O ( n s + min { m p , m log m + p ( n - p ) } ) time while preserving the linear space bound,...