Title :
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
Author :
Huang, Chao-Wen ; Lee, Wun-Shiun ; Hsieh, Sun-Yuan
Author_Institution :
Dept. of Comput. Sci. & Inf. Eng., Nat. Cheng Kung Univ., Tainan, Taiwan
Abstract :
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.
Keywords :
DNA; bioinformatics; molecular biophysics; search problems; DNA functional site discovery task; DNA sequences; heuristic algorithm; motif finding algorithm; planted (l,d)-motif search problem; real biological data set; Approximation algorithms; Bioinformatics; Computational biology; DNA; Heuristic algorithms; Search problems; (l; Planted motif search problem; d)-signals.; heuristic algorithms; Algorithms; Animals; Base Sequence; Binding Sites; Cattle; Chickens; Computational Biology; Computer Simulation; Consensus Sequence; DNA; Humans; Mice; Molecular Sequence Data; Nucleic Acid Conformation; Pattern Recognition, Automated; Sequence Analysis, DNA; Swine; Tetraodontiformes;
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
DOI :
10.1109/TCBB.2010.92
