Titlebook: Combinatorial Pattern Matching; 15th Annual Symposiu Suleyman Cenk Sahinalp,S. Muthukrishnan,Ugur Dogru Conference proceedings 2004 Springe

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Optimizing Multiple Spaced Seeds for Homology Search,s can have better sensitivity and specificity than single seeds. We describe a linear programming-based algorithm to optimize a set of seeds. Our algorithm offers a performance guarantee: the sensitivity of a chosen seed set is at least 70% of what can be achieved, in most reasonable models of homol

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Approximate Labelled Subtree Homeomorphism,entire subtrees, as well as repeatedly removing a degree-2 node and adding the edge joining its two neighbors. In this paper we extend the Subtree Homeomorphism Problem to a new optimization problem by enriching the subtree-comparison with node-to-node similarity scores. The new problem, denoted . (

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Approximate Point Set Pattern Matching on Sequences and Planes, the pattern to a subset of the text. We introduce an approximate point set pattern matching for axis-sorted point sequences that allows a translation, space insertions and deletions between points. We present an approximate pattern matching algorithm that runs with pattern size . and text size . in

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A Trie-Based Approach for Compacting Automata,tionaries for data compression and does not need to retain the input string, differently from other methods based on compact automata. The net effect is that of obtaining a lighter automaton than the directed acyclic word graph (DAWG) of Blumer et al., as it uses less nodes, still with arcs labeled

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