imgt2aa

extract aligned amino acid sequences from IMGT/HLA

Prerequisites

Need to first pull the hla.xml file

$ curl ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/xml/hla.xml.zip -o hla.xml.zip
$ unzip hla.xml.zip

Run

Note the database version (e.g. 3.56.0).

$ perl imgt2aa.pl  -v 3.56.0

Or run the full workflow:

$ ./run-quarterly.sh -v 3.65.0

Generates output files:

data/
    HLA-A.db
    HLA-B.db
    HLA-C.db
    HLA-DRB1.db
    HLA-DQB1.db
    HLA-DPB1.db

Each output file is tab-delimited with:

• locus
• allele (first 2 fields)
• amino acid sequence presented such that the position in the string corresponds to the position in the mature protein

Quarterly

Run this to create the .sap and KIR files.

./quarterly.pl -v 3.56.0

The driver script supports common cases:

./run-quarterly.sh -v 3.65.0
./run-quarterly.sh -v 3.65.0 -e
./run-quarterly.sh -v 3.65.0 --skip-download

How it works

The hla.xml file contains nucleotide sequences and cDNA coordinates for HLA alleles. The nucleotides for Exon2 are extracted and parsed. Then the cDNA coordinates are used to offset the AA sequence such that the first position in the string (possibly "*") corresponds to AA 1 in the mature protein.

TODO

• Complete implementation for all loci. Only implemented for A, B, C, DRB1, DQB, DPB1
• Incorporate other exons. Only implemented for ARS exons
• Address reading frame on the 3' end ("-")
• generalize to work with GFE defined alleles (a superset of IMGT/HLA)
• move to .DAT file which has BioPython support
• Get it to work with KIR and other loci

Martin Maiers mmaiers@nmdp.org