In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formal...
Abstract. The Knuth-Morris-Pratt (KMP) pattern-matching algorithm guarantees both independence from alphabet size and worst-case execution time linear in the pattern length; on the...
Frantisek Franek, Christopher G. Jennings, William...
Gene structure prediction is one of the most important problems in computational molecular biology. It involves two steps: the first is finding the evidence (e.g. predicting spl...
Abstract. The efficiency of regular expression matching algorithms depends very much on the size of the nondeterministic finite automata (NFA) obtained from regular expressions. R...
We present efficient sensitivity-analysis algorithms for two problems involving Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungap...