Download executable files for Windows and Linux

Version 2.2

Version 2.1

Version 2.0

Version 1.0

User manual can be found below

Source code can be found below

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, 9(4):1-22, 2014.

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

Download sample test results

Datasets for Comparison Results (Version 2.2) Results (Version 2.1) Results (Version 2.0) Results (Version 1.0)
W-ChIPMotifs_DM230.txt
RSAT_peak-motifs_DM230.txt
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
Results
Results Without Motif's Details
PScanChIP_DM05.txt
RSAT_peak-motifs_DM05.txt
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
Results
Results Without Motif's Details
MEME-ChIP_DM721.txt
PScanChIP_DM721.txt
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
Results
Results Without Motif's Details
DREME_DM230.txt
MEME_DM230.txt
PScanChIP_DM230.txt
RSAT_peak-motifs_DM230.txt
W-ChIPMotifs_DM230.txt
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
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
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
Results
Results Without Motif's Details
DREME_DM721.txt
MEME-ChIP_DM721.txt
PScanChIP_DM721.txt
RSAT_peak-motifs_DM721.txt
Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Motif Tree in HTML
Motif Tree in PDF
Motif Tree for Global Matching in HTML
Motif Tree for Global Matching in PDF
Motif Tree in PNG Image
Motif Tree for Global Matching in PNG Image

Input Motifs in Text
Results in HTML
Results in PDF
Results in Text
Results Without Motif's Details in Text
Results for Database Matching in HTML
Results for Database Matching in PDF
Results for Database Matching in Text
Results for Database Matching Without Motif Details in Text
Global Matching Results in HTML
Global Matching Results in PDF
Global Matching Results in Text
Global Matching Results Match with Database in HTML
Global Matching Results Match with Database in PDF
Global Matching Results Match with Database in Text
Combined Motifs for Global Matching in Text
Combined Motifs for Global and Local Matching in Text
Combined Motifs for Best Matches in Text
Phylogenetic Tree in HTML
Phylogenetic Tree in PDF
Phylogenetic Tree for Global Matching in HTML
Phylogenetic Tree for Global Matching in PDF
Phylogenetic Tree in PNG Image
Phylogenetic Tree for Global Matching in PNG Image

Input Motifs
Results
Results Without Motif's Details
Global Matching Results
Results
Results Without Motif's Details

Last updated on 06/18/2018.