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:
- motifsim_v1-0-linux32, tested on Linux 32 bits system.
- motifsim_v1-0-linux64, tested on Linux 64 bits system.
- motifsim_v1-0-wins32, tested on Windows 32 bits system.
- motifsim_v1-0-wins64, tested on Windows 64 bits system.
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 |