nmdp-bioinformatics/imgt2aa

Name: imgt2aa

Owner: NMDP/Be The Match Bioinformatics Research

Description: extract aligned amino acid sequences from IMGT/HLA

Created: 2017-06-21 04:12:15.0

Updated: 2017-06-21 04:28:21.0

Pushed: 2017-06-22 18:31:26.0

Homepage: null

Size: 8

Language: Perl

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README

imgt2aa

extract aligned amino acid sequences from IMGT/HLA

Prerequisites

Need to first pull the hla.xml file

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

Run

rl imgt2aa.pl >DPB1.db

The 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

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 DPB1
• Incorporate other exons. Only implemented for exon 2
• Address reading frame on the 3' end (“-“)
• generalize to work with GFE defined alleles (a superset of IMGT/HLA)
• Get it to work with KIR and other loci

Martin Maiers mmaiers@nmdp.org