## Example data for SLiM Discovery
The attached data can be used for testing the SLiM discovery tools of [SLiMSuite](https://github.com/slimsuite/SLiMSuite/).
```
315B POL30.Scer.apid-hq.acc
697K POL30.Scer.apid-hq.dat
35K POL30.Scer.apid-hq.fas
74M uniprot.yeast.147537.2019-05-14.fas.gz
50K elm2019.motifs
69K elm2019.split.motifs
39K elm2019.reduced.motifs
210B LIG_PCNA_PIPBox_1.motif
```
Example usage can be found in the [SLiMSuite CookBook](https://github.com/slimsuite/SLiMSuite/wiki/docs_md/CookBook.md).
### POL30 interactors
The `POL30.Scer.apid-hq.*` files are three different formats of "high quality" interactors with _Saccharomyces cerevisiae_ protein POL30 (human PCNA orthologue) from the [APID](http://cicblade.dep.usal.es:8080/APID/init.action) interaction database:
* `*.acc` = Uniprot accession numbers.
* `*.dat` = Full uniprot flat file.
* `*.fas` = Protein fasta file in [SLiMSuite format](http://slimsuite.blogspot.com/2015/10/file-format-fasta-seqfile-fasfile.html).
These represent alternative input formats for the same data.
### Yeast proteomes
The larger `uniprot.yeast.147537.2019-05-14.fas.gz` file is a gzipped fasta format of yeast proteomes downloaded from Uniprot on `2019-05-14`. This are all Uniprot proteomes for the [Saccharomycotina (true yeasts)](https://www.uniprot.org/taxonomy/147537) subphylum (TaxID:147537). Two proteomes with non-specific (`9XXXX`) species codes have been filtered out.
These data are provided for using [GOPHER](http://rest.slimsuite.unsw.edu.au/gopher) to generate predicted orthologue alignments for conservation masking.
### ELM Data
[ELM](http://elm.eu.org) motif classes (downloaded `2019-05-02`) are provided in the `elm2019.motifs` file. The `elm2019.split.motifs` file contains the same data split into different motif variants. SLiMSuite will generate this file when required if it does not already exist.
`elm2019.reduced.motifs` contains a "reduced" set of ELM class definitions, generated using [SLiMMaker](http://rest.slimsuite.unsw.edu.au/slimmaker) as described in the [QSLiMFinder paper](https://www.ncbi.nlm.nih.gov/pubmed/25792551?dopt=Abstract) by aligning ELM instances for that motif and then extracting a regular expression motif pattern from the alignment. Reduced ELM definitions lose a lot of the complexity and curator-derived knowledge. They are primarily useful as a test dataset of "True Positive" motifs that should be recoverable from sets of ELM instance proteins, but may also be useful for cleaner [CompariMotif](http://rest.slimsuite.unsw.edu.au/comparimotif) screens for known motif due to their reduction in complexity.
`LIG_PCNA_PIPBox_1.motif` contains a single motif for simplified examples.
### References
**Gouw M1 et a;.**
The eukaryotic linear motif resource - 2018 update.
[_Nucleic Acids Res._ 46:D428-D434 (2018)](https://www.ncbi.nlm.nih.gov/pubmed/29136216)
**The UniProt Consortium.**
UniProt: a worldwide hub of protein knowledge.
[_Nucleic Acids Res._ 47: D506-515 (2019)](https://doi.org/10.1093/nar/gky1049)
