You can obtain the PMut2017 predictions together with the set of numerical features which the predictions are based on. These features are accessible programatically in CSV (Comma Separated Values) format.
You can obtain the predictions of all possible mutations in a protein, but also the predictions of all mutations in a position or a specific variant:
URL format | Example link | Description |
---|---|---|
/PMut/uniprot/{UniProt_identifier}/features.csv
| /PMut/uniprot/P13807/features.csv | Predictions and features of all the variants of a protein. |
/PMut/uniprot/{UniProt_identifier}/{position}features.csv
| /PMut/uniprot/P13807/34/features.csv | Predictions and features of all variants in a position of a protein. |
/PMut/uniprot/{UniProt_identifier}/{position}/{mutated_type}/features.csv
| /PMut/uniprot/P13807/34/A/features.csv | Predictions and features of one variant. |
All the data related to a protein that is displayed in a protein page can also be accessed in JSON format through the API. This information includes UniProt annotations, sequence, known variants and their predictions, links to other related services and tools, etc. As before, this information can be accessed on a protein, position or variant level.
URL format | Example link | Description |
---|---|---|
/PMut/uniprot/{UniProt_identifier}.json
| /PMut/uniprot/P13807.json | Information related to a protein. |
/PMut/uniprot/{UniProt_identifier}/{position}.json
| /PMut/uniprot/P13807/34.json | Information related to a protein position. |
/PMut/uniprot/{UniProt_identifier}/{position}/{mutated_type}.json
| /PMut/uniprot/P13807/34/A.json | Information related to variant. |
The most important features for the prediction are based on sequence conservation. These features are extracted from different PSI-Blast searches over UniRef100 and UniRef90 cluster databases, and also from Multiple Sequence Alignments performed using Kalign2.
You can access all these files from the following URLs:
URL format | Example link | Description |
---|---|---|
/PMut/blast/{UniRef100_identifier}.100.xml.gz
| /PMut/blast/UniRef100_P13807.100.xml.gz | Result of PSI-Blast search over UniRef100. |
/PMut/blast/{UniRef100_identifier}.90.xml.gz
| /PMut/blast/UniRef100_P13807.90.xml.gz | Result of PSI-Blast search over UniRef90. |
/PMut/fa/{UniRef100_identifier}.100.fa.gz
| /PMut/fa/UniRef100_P13807.100.fa.gz | Input for MSA based on the PSI-Blast search results over UniRef100. |
/PMut/kalign/{UniRef100_identifier}.100.afa.gz
| /PMut/kalign/UniRef100_P13807.100.afa.gz | Multiple Sequence Alignment results using Kalign2 (over UniRef100 search). |
/PMut/fa/{UniRef100_identifier}.90.fa.gz
| /PMut/fa/UniRef100_P13807.90.fa.gz | Input for MSA based on the PSI-Blast search results over UniRef90. |
/PMut/kalign/{UniRef100_identifier}.90.afa.gz
| /PMut/kalign/UniRef100_P13807.90.afa.gz | Multiple Sequence Alignment results using Kalign2 (over UniRef90 search). |