The latest version of the alignment tool now includes genomic sequences as well alignments of commonly sequenced regions. Where discrepancies have arisen between reported sequences and those stored in the database, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and the WHO Nomenclature Committee would welcome any evidence that helps to maintain the accuracy of these sequence alignments.

STEP 1 - Select the gene and feature to align

STEP 2 - Select sequences and reference




STEP 3 - Select how you view the alignment




STEP 4 - Proceed with the alignment

Help with the Sequence Alignment Tool

  • Specific Sequences are optional, to align specific sequences either enter the common nomenclature or list the allele names separated by a comma. Do not include the locus in the name. Wildcards are automatically added to the codes unless you select the box to the right, which matches exactly to what is entered. For example, when aligning HLA-A, 02:12 would match to A*02:12 and A*02:120 to A*02:129, unless the check box was selected. Please note if the check box is selected the full allele name is required, for HLA-A, 02:01:01:01 would be needed and not simply 02.
  • Genomic alignments can contain over 1.5 million bases if all sequences are selected and displaying this many characters is time consuming, please be patient. Where possible select only the sequences needed, this will reduce time and make the alignments easier to view.
  • Specific sequences cannot be selected in multi-locus alignments like DRB1,3,4,5, DRB2,6,7,8,9 and DRB1-9.
  • The default reference sequence for all genes is automatically provided. An alternative reference sequence may be defined by entering the numerical part of the allele name into the text box. The full numerical code is required, so for A*01:01:01:01, this would be 01:01:01:01 and not 01:01.
  • Splice site variations have previously not been marked for alternatively spliced alleles like A*01:11N, A*03:01:01:02N, A*29:01:01:02N, B*15:01:01:02N and B*44:02:01:02. In order to rectify this we have now implemented a procedure for marking up these regions in alleles containing alternative splice sites. Sequence highlighted in grey, represents sequence that is affected by this, further details can be found here.
  • If you wish to view a consensus sequence of the alleles selected enter "CONSENSUS" in the box provided.
  • You may need to widen your browser to view the output. If you need to alter the size of the text use 'Ctrl' and '+' or '-' on a PC or 'Apple' and '+' or '-' on Mac. These keys may vary depending on your choice or browser.
  • Where discrepancies have arisen between reported sequences and those stored in the database, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and the WHO Nomenclature Committee would welcome any evidence that helps to maintain the accuracy of these sequence alignments.
  • The alignment tool uses a cookie to store the alignment parameters used. This cookie only contains these variables and is deleted at the end of your browser session. If you do not wish to accept this cookie you will have to re-enter the parameters each time you do an alignment. Internet Explorer uses should be aware that a bug has been reported in the javascript that automatically retrieves stored alignment parameters.

Further more detailed help can be found in the help file which details both the input options and how the alignments are displayed.

IMGT/HLA

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