Comparision Of DNA Motif Discovery Tools In ChIP-seq

The popularization of next-generation sequencing made motif discovery coexistence of opportunity and challenge. Especially the Ch IP-seq technology leads to a bulking data sets and data complexity. Numerous tools are currently available to extract binding motifs from peak calling data sets.The purpose of this work is to provide some guidance to users regarding the performance of the tools in Model Organism data sets. Thus 6 soft wares MEME, DREME, CHIPMUNK, RSAT-peak motif, HOMER and SIOMICS are picked out。37 real data sets of 4 species Mus musculus, Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae were used to test the computational time, number of motifs, distribution of motif length, and 4 simulated data sets were used to test the accuracy of them.We find that among the 4 species data sets, MEME program plays best on Saccharomyces cerevisiae data sets at 67.7%. While in the other species Homo sapiens, Mus musculus and Drosophila melanogaster, HOMER plays best at about 30%. Meanwhile, we believe that the coverage of results cannot replace the accuracy to be the determine index.