MOTIFSIM: Tool for Detecting Similarity in Multiple DNA Motif Datasets

MOTIFSIM is a software tool for detecting similarity in multiple motif datasets. It accepts nine different motif input formats and outputs the results in two text files. Please, consult the user manual for using this tool.

Current version: v. 1.0

Download executable files for Windows and Linux:

User manual can be found here .

Source code for compiling with make can be found here .

Download test datasets:

Test datasets came from original publication: N.T.L. Tran and C.-H. Huang, “A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data“, Biology Direct, vol. 9, pp. 1-22, 2014.

Motif Dataset Motif Input Format Number of Motifs
DREME_DM230.txt MEME’s output 1
MEME_DM230.txt MEME’s output 20
PScanChIP_DM230.txt Jaspar 14
RSAT_peak-motifs_DM230.txt TRANSFAC-like 10
W-ChIPMotifs_DM230.txt PSSM 11
MEME_DM05.txt MEME’s output 46
MEME-ChIP_DM05.txt MEME’s output 4
PScanChIP_DM05.txt Jaspar 16
RSAT_peak-motifs_DM05.txt TRANSFAC-like 17
W-ChIPMotifs_DM05.txt PSSM 11
DREME_DM721.txt MEME’s output 16
MEME-ChIP_DM721.txt MEME’s output 11
PScanChIP_DM721.txt Jaspar 37
RSAT_peak-motifs_DM721.txt TRANSFAC-like 40

Download sample test results:

Datasets for Comparison Results
W-ChIPMotifs_DM230.txt
RSAT_peak-motifs_DM230.txt
Results
Results Without Motif’s Details
PScanChIP_DM05.txt
RSAT_peak-motifs_DM05.txt
Results
Results Without Motif’s Details
MEME-ChIP_DM721.txt
PScanChIP_DM721.txt
Results
Results Without Motif’s Details
DREME_DM230.txt
MEME_DM230.txt
PScanChIP_DM230.txt
RSAT_peak-motifs_DM230.txt
W-ChIPMotifs_DM230.txt
Results
Results Without Motif’s Details
MEME_DM05.txt
MEME-ChIP_DM05.txt
PScanChIP_DM05.txt
RSAT_peak-motifs_DM05.txt
W-ChIPMotifs_DM05.txt
Results
Results Without Motif’s Details
DREME_DM721.txt
MEME_DM721.txt
PScanChIP_DM721.txt
RSAT_peak-motifs_DM721.txt
Results
Results Without Motif’s Details
Last updated on 09/15/2014.