An improved heuristic algorithm for finding motif signals in DNA sequences.
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.
Huang
Chao-Wen
CW
Department of Computer Science and Information Engineering, National Cheng Kung University, No. 1, University Road, Tainan 70101, Taiwan. huangcw@csie.ncku.edu.tw
Lee
Wun-Shiun
WS
Hsieh
Sun-Yuan
SY
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002417:Cattle; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010363:Pattern Recognition, Automated / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013552:Swine; D023721:Tetraodontiformes
D004247:DNA