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Computer Modeling of Molecular Genetic Events using Content Sensitive Analysis

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Title: Computer Modeling of Molecular Genetic Events using Content Sensitive Analysis
Author: Stodgell, Curtis
Issue Date: 2007
Publicly Available in cIRcle 2010-07-30
Series/Report no. University of British Columbia, Okanagan campus, Computer Science Undergraduate Honours Essays
Abstract: The problem of motif finding plays an important role in understanding the development, function and evolution of organisms. The Planted (l, d)-Motif Problem first introduced by Pevzner and Sze [13] is a variant model of motif finding that has been widely studied. Nevertheless, despite the many different algorithms constructed to solve this problem, it is far from being solved entirely [5]. We analyze a number of algorithms including: the Basic Voting Algorithm, the Winnower and the Closest String. One thing that has become ubiquitous among these algorithms is the tradeoff between efficiency and accuracy. We formulate the motif-finding problem as a constraint satisfaction problem and introduce a special form of constraint consistency. By using a fixed-parameter algorithm for the closest string problem [4], we develop a propagation algorithm that enforces the new constraint consistency with the same worst-case time complexity as that of the standard path consistency algorithm. Experiments on randomly generated sequences indicate that our approach is effective and efficient.
Affiliation: Psychology and Computer Science (PSCS) (IKBSAS) (Okanagan)
URI: http://hdl.handle.net/2429/27050
Peer Review Status: Unreviewed

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