Answers.Body: <p>These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository.</p>
  
  <p>A*11:01 has very high frequency in Aborigine populations <a href="http://www.allelefrequencies.net/hla6006a.asp?hla_locus_type=Classical&amp;hla_locus=&amp;hla_allele1=A*11%3A01&amp;hla_allele2=A*11%3A01&amp;hla_selection=&amp;hla_pop_selection=&amp;hla_population=&amp;hla_country=&amp;hla_dataset=&amp;hla_region=&amp;hla_ethnic=&amp;hla_study=&amp;hla_order=order_1&amp;hla_sample_size_pattern=equal&amp;hla_sample_size=&amp;hla_sample_year_pattern=equal&amp;hla_sample_year=&amp;hla_level_pattern=equal&amp;hla_level=&amp;standard=a&amp;hla_show=" rel="nofollow noreferrer">here</a> . You can explore the population genetics and the past, present and current population genetics distributions per population of HLA at <a href="http://www.allelefrequencies.net/" rel="nofollow noreferrer">http://www.allelefrequencies.net/</a> </p>
  
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Answers.CreationDate: 2019-03-19T14:14:22.140Z
Answers.Text: 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. :)
Answers.UserDisplayName: Guy Coder
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Answers.CreationDate: 2019-03-19T14:42:00.923Z
Answers.Text: Thanks, I would look at whether these alleles cluster geographically. Secondly, the diseases which induce high HLA*11:  alleles
Answers.UserDisplayName: M__
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Answers.CreationDate: 2019-03-19T14:47:04.027Z
Answers.Text: 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.
Answers.UserDisplayName: Guy Coder
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-19T22:44:31.207Z
Answers.Text: 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)
Answers.UserDisplayName: M__
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Answers.CreationDate: 2019-03-19T13:53:28.097Z
Answers.LastActivityDate: 2019-03-19T13:53:28.097Z
Answers.UserDisplayName: M__
Body: <p>In creating a parser for the UniProt flat file <code>uniprot_sprot.dat</code> (<a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/" rel="nofollow noreferrer">directory</a>) in the <a href="https://www.uniprot.org/docs/userman.htm" rel="nofollow noreferrer">manual</a> for the comments <code>POLYMORPHISM</code> there are listed patterns for alleles, e.g. for <code>1A11_HUMAN</code> is </p>
  
  <blockquote>
    <p>The following alleles of A-11 are known:<br>
    A*11:01 (A-11E), A*11:02 (A-11K), A*11:03, A*11:04, A*11:05 and A*11:07.</p>
  </blockquote>
  
  <p>I tried searching for a description of the patterns using the words <code>allele</code> and/or <code>polymorphism</code> and found nothing.</p>
  
  <ul>
  <li>How are the allele patterns to be interpreted?  </li>
  <li>Is there a search term to be used when looking for the patterns?  </li>
  <li>Also, is there an official repository of the alleles?</li>
  </ul>
  
  <p>The answer does not have to explain the specifics of the example given.</p>
  
  <hr>
  
  <p>Example of explanation of other allele pattern from <a href="http://hla.alleles.org/nomenclature/naming.html" rel="nofollow noreferrer">here</a></p>
  
  <p><a href="https://i.sstatic.net/jZhwr.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/jZhwr.png" alt="enter image description here"></a></p>
  
  <p>This explanation of the patterns doesn't explain the part of the pattern in UniProt like <code>(A-11E)</code>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-19T11:41:58.533Z
Comments.Text: Of interest: [Nomenclature for Factors of the HLA System](http://hla.alleles.org/nomenclature/naming.html)
Comments.UserDisplayName: Guy Coder
Tags: <phylogenetics><phylogeny><file-formats><uniprot>
Title: How to interpret UniProt allele patterns?
ThreadText: # How to interpret UniProt allele patterns?
  
  (Asked by: username_0 on 2019-03-19)
  
  In creating a parser for the UniProt flat file `uniprot_sprot.dat` ([directory](ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/)) in the [manual](https://www.uniprot.org/docs/userman.htm) 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](http://hla.alleles.org/nomenclature/naming.html)
  
  [![enter image description here](https://i.sstatic.net/jZhwr.png)](https://i.sstatic.net/jZhwr.png)
  
  This explanation of the patterns doesn't explain the part of the pattern in UniProt like `(A-11E)`.
  
  **Tags:** phylogenetics, phylogeny, file-formats, uniprot
  
  > **Comments:**
  > **username_0**: Of interest: [Nomenclature for Factors of the HLA System](http://hla.alleles.org/nomenclature/naming.html)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-03-19. Score: 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](http://www.allelefrequencies.net/hla6006a.asp?hla_locus_type=Classical&hla_locus=&hla_allele1=A*11%3A01&hla_allele2=A*11%3A01&hla_selection=&hla_pop_selection=&hla_population=&hla_country=&hla_dataset=&hla_region=&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=equal&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_level_pattern=equal&hla_level=&standard=a&hla_show=) . You can explore the population genetics and the past, present and current population genetics distributions per population of HLA at <http://www.allelefrequencies.net/>
  
  > **Comments:**
  > **username_0**: 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. :)  
  > **username_1**: Thanks, I would look at whether these alleles cluster geographically. Secondly, the diseases which induce high HLA*11:  alleles  
  > **username_0**: 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.  
  > **username_1**: 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)  
  
  ---
  
  