Algorithmica

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On Almost Monge All Scores Matrices

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Abstract

The all scores matrix of a grid graph is a matrix containing the optimal scores of paths from every vertex on the first row of the graph to every vertex on its last row. This matrix is commonly used to solve diverse string comparison problems. All scores matrices have the Monge property, and this was exploited by previous works that used all scores matrices for solving various problems. In this paper, we study an extension of grid graphs that contain an additional set of edges, called bridges. Our main result is to show several properties of the all scores matrices of such graphs. We also apply these properties to obtain an \(O(r(nm+n^2))\) time algorithm for constructing the all scores matrix of an \(m\times n\) grid graph with r bridges and bounded integer weights.

Keywords

Sequence alignment Longest common subsequences DIST matrices Monge matrices All path score computations Multiple-source shortest-paths 

Notes

Acknowledgements

We thank the anonymous reviewers, that helped us improve the readability of the paper through their many helpful suggestions. The research of A.C and D.T was partially supported by ISF Grant No. 981/11. The research of A.C and M.Z-U was partially supported by ISF Grant 179/14.

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Computer ScienceBen-Gurion University of the NegevBeershebaIsrael

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