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The Gene Feature Enumeration (GFE) Submission service provides an API for converting raw sequence data to GFE. It provides both a RESTful API and a simple user interface for converting raw sequence data to GFE results. Sequences can be submitted one at a time or as a fasta file. This service uses nmdp-bioinformatics/service-feature for encoding the raw sequence data and nmdp-bioinformatics/HSA for aligning the raw sequence data.
The GFE allele name is created by joining the feature accession numbers. Each accession number is generated by making a RESTful call to the feature service with the sequence and it’s corresponding feature. If the sequence has been observed before, then the feature service will return the previously generated accession number, otherwise it will generate a unique accession number for that feature and return it. The GFE allele HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1 is broken up into the following parts:
Feature Accession Number
five_prime_UTR 1
Exon 1 1
Intron 1 7
Exon 2 20
Intron 2 10
Exon 3 32
Intron 3 7
Exon 4 1
Intron 4 1
Exon 5 1
Intron 5 6
Exon 6 1
Intron 6 5
Exon 7 3
Intron 7 5
Exon 8 1
three_prime_UTR 1
In the example above all of the features for HLA-A were found in the sequence. If a sequence does not contain a particular feature, then the feature accession number will be zero. The raw sequence is broken up into each of its features using the annotation pipeline.
- A gene feature enumeration approach for describing HLA allele polymorphism
- Public version of service: gfe.b12x.org
- More detailed documentation on GFE service
- IGDAWG Website
- Feature service
- https://bioinformatics.bethematchclinical.org/
- https://github.com/nmdp-bioinformatics/HSA
- https://github.com/nmdp-bioinformatics/service-feature
- https://hub.docker.com/r/nmdpbioinformatics/service-gfe-submission/