Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of each gene; what is the name of this type of alignment format? sample:

# file: A_gen.txt
# date: 2020-07-13
# version: IPD-IMGT/HLA 3.41.0
# origin: http://hla.alleles.org/wmda/A_gen.txt
# repository: https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/alignments/A_gen.txt
# author: WHO, Steven G. E. Marsh (steven.marsh@ucl.ac.uk)
 gDNA              -300
 A*01:01:01:02N    ********** ********** ********** ********** ********** ********** ********** *********- ---------- ---------- 
 A*01:01:01:03     ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- 
 A*01:01:01:04     ********** ********** ********** ********** ********** ********** ********** ********** ********** ********** 

There is the .msf format of the same dataset at, HLA gene A in .msf format, git repo, and there are 2 types of characters in the data [A,C,G,T,.], where the '.' denotes the gap (correct?). For this above, unknown to me, format there are 3 extra symbols, [A,C,G,T,.,$*$,|,_]. I assume that the symbol '|' (pipe character) is for the exon, then what do the symbol characters $'*'$, '$\_$', and '.' denote in this format? I assume that the '.' still denotes the gap, so what is the $'*'$ and '$\_$'? Does $'*'$ reference missing data in terms of the reference sequence? If so the .msf format lacks this information? and would it be reasonable to assume that '$\_$' is that the data at that base pair is equal to the reference sequence as sequence 1?

If my assumption is correct and this new dataset accounts for 'missing genomic data' in the alignment and the msf does not, then the .msf is penalizing with a gap data that is actually missing?

(the FASTA data for this gene, link to the fasta file, shows that the reads for allele are of a different length)


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