Comparison and Analysis on Subtle Motifs Discovery Algorithms in DNA Sequence

Finding motifs is a significant computational problem in bioinformatics,many models and algorithms have been proposed to solve this problem.By reason of the complexity of DNA sequence data,there exist lots of subtle motifs which are much more difficult to be found than strong signals.Up to now,the planted(l,d) motif problem and the extended planted(l,d) motif problem are two suitable models for finding subtle motifs.This paper generalizes and analyzes the methods and strategies of motif discovery and the motif model as well as points out their advantages and disadvantages.Based on the above work,this paper further assays some main present subtle motif discovery algorithms through experiments and make a reference for the users of motif discovery.This paper also provides discussion on some unresolved problems and development trend in this field.