Motif Finding
| Name | Description | Sequence Type* | Link |
|---|---|---|---|
| PMS | Motif search and discovery | Both | server server |
| FMM | Motif search and discovery (can get also positive & negative sequences as input for enriched motif search) | Nucleotide | server |
| BLOCKS | Ungapped motif identification from BLOCKS database | Both | server |
| eMOTIF | Extraction and identification of shorter motifs | Both | servers |
| Gibbs motif sampler | Stochastic motif extraction by statistical likelihood | Both | server server |
| HMMTOP | Prediction of transmembrane helices and topology of proteins | Protein | homepage & download |
| I-sites | Local structure motif library | Protein | server |
| JCoils | Prediction of Coiled coil and Leucine Zipper | Protein | homepage & download |
| MEME/MAST | Motif discovery and search | Both | server |
| CUDA-MEME | GPU accelerated MEME (v4.4.0) algorithm for GPU clusters | Both | homepage |
| MERCI | Discriminative motif discovery and search | Both | homepage & download |
| PHI-Blast | Motif search and alignment tool | Both | Pasteur |
| Phyloscan | Motif search tool | Nucleotide | server |
| PRATT | Pattern generation for use with ScanProsite | Protein | server |
| ScanProsite | Motif database search tool | Protein | server |
| TEIRESIAS | Motif extraction and database search | Both | server |
Read more about this topic: List Of Sequence Alignment Software
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