The latest version of the alignment tool now includes genomic sequences as well alignments of commonly sequenced regions (e.g. specific exons and introns).

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*15:01:01:02N and B*44:02:01:02S 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

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