Titlebook: Algorithms in Bioinformatics; Third International Gary Benson,Roderic D. M. Page Conference proceedings 2003 Springer-Verlag Berlin Heidel

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Theoretisch-methodische Anlage der Studieices such that the likelihood of generating both the ancestral and contemporary sequences is maximized. Our NP-hardness proof follows that for MP given in (Day, Johnson and Sankoff, 1986) in that we use the same reduction from .; however, the proof of correctness for this reduction relative to AML is different and substantially more involved.

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Common Intervals of Two Sequenceserties of common intervals between two general sequences. We bound the maximum number of common intervals between two sequences of length . by .. and present an .(..log(.)) time complexity algorithm to enumerate their whole set of common intervals. This complexity does not depend on the size of the alphabets of the sequences.

excrete

Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functionsvalency sets in both cases..We describe the algorithm, compare it to other algorithms and give the results of the tests on discovering binding sites for DNA-binding proteins (ArgR, LexA, PurR, TyrR respectively) in ., and promoter sites in a set of Dicot plants.

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A Local Chaining Algorithm and Its Applications in Comparative Genomicsing methods from computational geometry. A variant of the algorithm finds all significant local chains of colinear non-overlapping fragments. The local chaining algorithm can be used in a variety of problems in comparative genomics: The identification of regions of similarity (candidate regions of c

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