Database Support

This module contains features for accessing databases containing protein related data.

Pfam

The following functions can be used to search and retrieve Pfam data:

• fetchPfamMSA() - download MSA files
• searchPfam() - search for domain families of a protein

UniProt

The following functions and class can be used to search and retrieve UniProt data:

• queryUniprot() - query UniProt and parse the results as a dictionary
• UniprotRecord - a wrapper from UniProt data with functions including parsing PDBs
• searchUniprot() - search UniProt and return a UniprotRecord

CATH

The following class and its functions can be used to search and retrieve CATH data:

• CATHDB - parse, handle and navigate the tree-like structure of the CATH database

DALI

The following class and functions can be used to search and retrieve data using the DALI structure alignment server:

• searchDali() - search for similar structures using DALI
• DaliRecord - fetch and handle outputs from DALI searches
• daliFilterMultimers() - filter DALI results to obtain multimers of a particular size

QuartataWeb

The following classes and functions can be used to search and retrieve data using the QuartataWeb structure alignment server:

• QuartataWebBrowser - class based on the Splinter web browser package to search QuartataWeb
• QuartataChemicalRecord - class to handle the outputs of QuartataWeb searches
• searchQuartataWeb() - perform QuartataWeb searches and return the output in a QuartataChemicalRecord

Gene Ontology Annotation (GOA)

The following classes and functions can be used to search and retrieve data from the EBI GOA database:

• queryGOA() - query GOA using a PDB ID
• GOADictList - class to handle data from GOA queries
• parseOBO() - parse an OBO file containing the Gene Ontology.
• parseGAF() - parse a Gene Association File (GAF)
• showGoLineage() - visualize GO tree
• calcGoOverlap() - Calculate overlap between GO terms from their distance in the graph

Interpro

The following functions can be used to search and retrieve Interpro data:

• searchInterpro() - search for domain families of a protein

BioExcel-CV19

The following functions can be used to retrieve BioExcel-CV19 data:

• fetchBioexcelPDB() - fetch PDB files for starting structures for trajectories