The alignment tool provides access to pre-compiled alignments for individual HLA genes and sequence features (e.g. specific exons and introns), or alignments of commonly sequenced regions (e.g. exons 2+3).

Align Beta

The IPD team are currently working on a new version of the alignment tool based on some of the recent developments utilised in the IPD-MHC and IPD-NHKIR projects. To try the new version of the tool please click the following link.

  1. Link to Beta Tool

Alignment Tool - Version 1

Please Note:

Due to the increasing number of full length sequences in the database this tool is no longer able to provide Genomic -
Full Length
alignments containing all alleles for some loci due to technical constraints. We advise that when selecting Genomic - Full Length alignments you specify individual alleles or allele groups. When specifying allele groups we recommend no more than 5 allele groups be included to be sure that the alignment will complete. If you require complete alignments we recommend either using the beta tool (link above) or download the text alignment files available from the ftp.

STEP 1 - Select the locus and features to align

STEP 2 - Specify reference and required sequences




STEP 3 - Select alignment display options




STEP 4 - Proceed with the alignment

Help with the Sequence Alignment Tool

  1. 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 names e.g. when aligning HLA-A, specifying "02:12" in the specific sequences box would match to A*02:12 and A*02:120 to A*02:129. If the exact matches box is ticked the full allele name is required e.g. for A*02:01:01:01 to appear in a HLA-A alignment, "02:01:01:01" would need to be specified and not simply "02".
  2. If all sequences are selected, genomic alignments can contain millions of bases and displaying this many characters is time consuming, so please be patient. Where possible, please select only the sequences required as this will reduce loading times and make the alignments easier to browse.
  3. Specific sequences cannot be selected in multi-locus alignments like DRB1,3,4,5, DRB2,6,7,8,9 and DRB1-9.
  4. 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 provided. The full numerical code is required, e.g. to specifiy A*01:01:01:01 as the reference sequence in a HLA-A alignment, please enter "01:01:01:01" into the reference sequence box.
  5. Splice site variants like A*01:11N, A*03:01:01:02N, A*29:01:01:02N, B*07:44N, B*15:01:01:02N, B*44:02:01:02S, B*56:01:01:05S, C*03:23N, C*15:02:01:08N and DRB4*01:03:01:02N are now marked up to show the affected parts of the respective sequences. In the CDS and/or Genomic alignments, the affected sequence is highlighted in green and a description of the alternative splicing is provided at the top of the page. Further details can be found here.
  6. If you wish to view a consensus sequence of specified alleles, type "CONSENSUS" into the reference sequece box (see point 4) and enter any specific alleles you desire (see point 1).
  7. You may need to widen your browser window or zoom out to view the alignments properly.
  8. Discrepancies between reported sequences and those stored in the database may arise. In these cases, the original authors will be contacted where possible and necessary amendments to published sequences will be incorporated into the alignments. Future sequencing methods may identify errors in older sequences and the WHO Nomenclature Committee for Factors of the HLA System welcomes any evidence that helps maintain the accuracy of the sequences held in the IPD-IMGT/HLA Database.
  9. The alignment tool uses cookies to store the alignment parameters used, and nothing else. The cookies are deleted at the end of your browser session. If you do not wish to accept cookies, 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.
  10. Due to the number of alleles included and issues with viewing the alignments, as of Release 3.33.0, it is no longer possible to provide a Class I alignment online.

Further help and details of the input options and how the alignments are displayed can be found in here.

Further Information

For more information about the database, queries (including website) or to subscribe to the IPD mailing lists please contact IPD Support.

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