CompariMotif provides a number of pre-defined motif datasets in the correct format for use. When using results from these datasets, please always cite the relevant paper.
These datasets are given in the Table below. If you have additional motif databases you would like to see available, please contact me.
Database |
Description |
References |
| ELM [View File] [2008 Data] [2010 Data] |
The Eukaryotic Linear Motif database provides a number of high quality annotated SLiMs with known occurrences.
Note. Some motifs have been split into _a and _b to be compatible with CompariMotif input formats. Such motifs are marked *Modified* in their descriptions. |
Puntervoll P et al. (2003). "Elm server: A new resource for investigating short functional sites in modular eukaryotic proteins." Nucleic Acids Res 31(13): 3625-30. |
| MiniMotif 1.0 [View File] |
Another database of SLiMs from all organisms. This has less annotation than ELM but more motifs. These motifs have been reformatted to conform to standard regular expressions. |
Balla S et al. (2006). "Minimotif miner: A tool for investigating protein function." Nat Methods. 3(3): 175-7. |
| PhosphoMotif Finder [View File] |
Motifs from the PhosphoMotif Finder database of HPRD. Motifs are labelled KIN for Kinase / Phosphatase motifs or BIND for binding motifs.
_Y indicates a tyrosine motif, while _ST indicated serine/threonine. The number part of the motif identifier is arbitrary and has no link to the website.
Note. All these motifs are phosphorylation motifs and, as such, have a key Ser, Thr or Tyr position.
These are not given special treatment in CompariMotif and the user should pay special attention to whether the appropriate residue is included in the match. |
Puntervoll P et al. (2003). "Elm server: A new resource for investigating short functional sites in modular eukaryotic proteins." Nucleic Acids Res 31(13): 3625-30. |
| Miscellaneous Literature [View File] |
Miscellaneous motifs collected from the literature. (These include pubmed links to the relevant paper but we cannot guarantee the accuracy of the motifs or their descriptions.) |
See PubMed links in file. |
| Combined Literature [View File] |
A combined database of the above sources. The source database is indicated in the motif description: [ELM] for ELM, [MnM] for MiniMotif and [PMF] for PhosphoMotif Finder. |
See above. |
| Neduva et al. (2005) [View File] |
Predicted interaction SLiMs from the high-throughput study of Neduva et al. (2005). The motif name indicates what part of the study it is from.
All names begin NR, followed by a two-letter code for the species and a one-letter code denoting Domain-level datasets or Protein-level datasets. (See paper for details.)
Species codes are: Ce, C. elegans; Dm, D. melanogaster; Hs, H. sapiens; Sc, S. cerevisiae. |
Neduva V et al. (2005). "Systematic discovery of new recognition peptides mediating protein interaction networks." PLoS Biol. 3(12): e405. |
| All Databases. View File |
All of the data from the above databases merged.
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