PFQL - Protein Feature Query Language
PFQL is a flexible feature querying language for proteins. By feature we mean anything that can be identified in a protein sequence: transmembrane regions, domain models, signal peptides, low complex regions and more.
It works by inserting the field
PFQLMatches with the value of an array with the indexes of the matching definitions.
$ npm install pfql
Example of sets of rules:
let query =rules:Npos:resource: 'pfam28'feature: 'MCPsignal'
example of input data (
Then you can use as a service:
let pfql =let sampleData =let pfqlService = querypfqlServicesampleData
Or use it as a stream
let pfql =let pfqlStream = querypfqlStreamfs
Understanding the fundamentals of PFQL
Searching the protein universe with Domain architecture
It is our hypothesis that a more accurate search in the protein universe for members of a particular protein family can be achieved by searching based on protein features, in particular based on protein domains. As the accuracy, coverage and overall quality of protein domain models in several databases, prediction tools such as transmembrane region, we expect that defining protein families based on protein domains will be the ultimate method used in the future.
PFQL exposes two classes: PFQLStream and PFQLService
The PFLQStream is a
Transform stream that wraps the PFQLService for convenience. The constructor takes a set of matching rules that should describe the protein family of interest. For example, if the protein family of interest is the chemotaxis scaffold CheW, a possible rule would be
match all sequences that has only one CheW domain, as defined by Pfam 30 database. In reality, the
FQLStream can process multiple protein families definitions at once and therefore, the constructor takes an array of set of matching rules, each set for protein family. The rules must be initiated with the method
.initRules. The output is the same information as the input plus a field
FQLMatches with the indexes of the set of rules that this particular protein matches.
To learn more about how to setup rules, check out the manual