API

All the data in the repository is accessible programatically via an API.

Predictions and features

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.

Protein information

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.

Files used in the features computation

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).