Introduction of Algorithms and Performance Research of Softwares for Motif Discovery

Motif plays a key role in the gene-expression regulating on both transcriptional and post-transcriptional levels.(Nowadays) there are several algorithms and softwares on detecting Motif,but,however,there is few papers on comparing the performance of these algorithms and softwares.This paper comes up with this background to introduce the classification of the algorithms in general and three common algorithms: Wordup,MM,Gibbs sampling-in details.And a performance comparison is made on the thirteen softwares for Motif detecting such as AlignACE,MEME,MotifSampler,Weeder,etc.Based on the(biological) research and the performance report,this paper ends with a conclusion that Weeder is the most effective one of these softwares,for it is the only algorithm that takes account of the conserved core positions of Motifs;Most algorithms only consider simple and short Motifs,so their Motif detecting performance on monadic yeast is significantly higher than on metazoans.