Table 1. MEME Suite capabilities.
| Capability | meme Suite (17) | Consensus (18) | Gibbs Sampler (19) | RSAT (20) | Trawler (21) | W-ChIPMotifs (22) | MoDTools (23) | YMF 3.0 (24) | XXmotif (25) |
|---|---|---|---|---|---|---|---|---|---|
| DNA motif discovery | meme | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Protein motif discovery | meme | ✓ | ✓ | ||||||
| Probabilistic motif discovery | meme | ✓ | ✓ | ✓ | ✓ | ✓ | |||
| Discrete motif discovery | DREME | ✓ | ✓ | ✓ | |||||
| Arbitrary gaps in motifs | glam2, glam2scan | ✓ | |||||||
| Positionally constrained motifs | meme | ✓ | |||||||
| Discriminative PWM motif discovery | meme | ✓ | ✓ | ||||||
| Motif scanning | fimo, mcast, glam2scan | ✓ | ✓ | ✓ | ✓ | ||||
| Motif enrichment analysis | CentriMo, AME, SpaMo, gomo | ✓ | ✓ | ||||||
| Motif comparison | Tomtom | ✓ | |||||||
| Motif cluster & spacing analysis | SpaMo | ||||||||
| Motif functional role analysis | gomo | ||||||||
| ChIP-seq analysis | meme-chip | ✓ | ✓ | ✓ | ✓ | ✓ |
Comparison of MEME Suite capabilities with other web-based tools. Note that W-ChIPMotifs uses MEME for motif discovery. URLs of the servers are provided in the bibliography. The table does not include servers that require additional inputs, such as aligned orthologs, phylogenetic trees, microarray expression profiles or ChIP-chip data.