3

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there are listed patterns for alleles, e.g. for 1A11_HUMAN is

The following alleles of A-11 are known:
A*11:01 (A-11E), A*11:02 (A-11K), A*11:03, A*11:04, A*11:05 and A*11:07.

I tried searching for a description of the patterns using the words allele and/or polymorphism and found nothing.

  • How are the allele patterns to be interpreted?
  • Is there a search term to be used when looking for the patterns?
  • Also, is there an official repository of the alleles?

The answer does not have to explain the specifics of the example given.

Example of explanation of other allele pattern from here

enter image description here

This explanation of the patterns doesn't explain the part of the pattern in UniProt like (A-11E).

M__
  • 12,263
  • 5
  • 28
  • 47
Guy Coder
  • 315
  • 1
  • 9

1 Answers1

4

These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository.

A*11:01 has very high frequency in Aborigine populations here . You can explore the population genetics and the past, present and current population genetics distributions per population of HLA at http://www.allelefrequencies.net/

M__
  • 12,263
  • 5
  • 28
  • 47
  • Thanks. I gave it an up-vote, but I don't see how this answers my main question of How are the allele patterns to be interpreted? Also my background is in computer programming, so please don't take for granted I have knowledge on the bioinformatic information. :) – Guy Coder Mar 19 '19 at 14:14
  • Thanks, I would look at whether these alleles cluster geographically. Secondly, the diseases which induce high HLA*11: alleles – M__ Mar 19 '19 at 14:42
  • My goal is to try and parse the allele patterns further than what they currently are (strings of characters) so that the parser can validate that they are correct. Without the pattern the only way to verify them would be to check each one against an database. Even then the allele might be correct but not in the database. With a pattern there is a second means of validating the allele. – Guy Coder Mar 19 '19 at 14:47
  • HLA alleles should have been extensively characterised. I have a colleague that types this stuff alot, but I tend to avoid it ( complicated ethics applications) – M__ Mar 19 '19 at 22:44