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Issue No. 04 - July/August (2011 vol. 8)
ISSN: 1545-5963
pp: 959-975
Chao-Wen Huang , National Cheng Kung University, Tainan
Wun-Shiun Lee , National Cheng Kung University, Tainan
Sun-Yuan Hsieh , National Cheng Kung University, Tainan
The planted (l,d)-motif search problem is a mathematical abstraction of the DNA functional site discovery task. In this paper, we propose a heuristic algorithm that can find planted (l,d)-signals in a given set of DNA sequences. Evaluations on simulated data sets demonstrate that the proposed algorithm outperforms current widely used motif finding algorithms. We also report the results of experiments on real biological data sets.
Planted motif search problem, heuristic algorithms, (l, d)-signals.

W. Lee, S. Hsieh and C. Huang, "An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 959-975, 2010.
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