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Research on Projection Algorithm for the Motif Discovery Problem

Author: LiYingBin
Tutor: HuoHongWei
School: Xi'an University of Electronic Science and Technology
Course: Computer Software and Theory
Keywords: Bioinformatics Motif discovery Projection Criterion selection
CLC: TP391.41
Type: Master's thesis
Year: 2009
Downloads: 10
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Abstract


In the DNA sequence, the motif refers to the sequence fragment which is conservative. How to find these motifs from the DNA scquence is the motif discovery problem, which is an important content of the bioinformatics study.In this thesis, the basic methods of motif modeling, which are used in different kinds of motif discovery algorithms, are firstly reviewed. On the basis of the different models, the motif discovery algorithms are studied and compared. Then we focus on the random projection algorithm and the uniform projection algorithm. Compared to the random projection algorithm, the uniform projection algorithm replaces the random choice of projections with a greedy heuristic that approximately equalizes the coverage of chosen projections, and it has a better performance in the efficiency and accuracy. Finally, base on the criterion selection algorithm, a refined uniform projection algorithm is presented. In order to reduce the amount of enriched buckets for motif modeling and EM refine, those buckets which don’t satisfy the criterion inequalities are threw. By the mean, the algorithm’s performance is able to be improved. Theoretical analysis and experiment have shown that the algorithm can find motif correctly and has good performance in the motif discovery problem. Furthermore, the algorithm can be directly applied to other problems where the projection algorithm has been used, including comparison of protein sequence databases.

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