Amino Acid Alignment

Amino Acid Alignment

For each gene, amino acid sequences for all alleles were aligned together. Protein sequence alignments were downloaded from IMGT/HLA, the current release Release 3.23.0, 2016-01-19 was used.

Options

--file input0.txt　   [Mandatory]
--align                 [Mandatory]
--out output.txt        [Default]
--print                 [Optimal]
--consensus             [Optimal]

option --consensus

When low resolution HLA typing was used in the input file, the program takes the consensus string of all possible high-resolution HLA typings, marking polymorphic amino acid positions as unknown. For example, when C*06:53, which can not be found in the alignment file, was used as input, the consensus sequence of two (it is quite possible larger than two for other alleles) higher-resolution HLA typings C*06:53:01 and C*06:53:02 will be used. If --consensus was not specified, sequence of C*06:53:01 will be used as default.

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