Sequence Alignment Tool

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 Classic

Please Note:

Although we recommend following the link on the alignment results rather than using the browser's back button for navigation we appreciate that this can be time consuming when multiple similar alignments are being carried out. To help, this form will now allow you to select features when returning from a previous alignment.

We have tested this in Chrome, Safari and IE on both Mac and Windows platforms.

For more help regarding use of the sequence alignment tool please see our Alignment Help

Select the alignment options
Step 1Select locus
Step 2Select features
Step 3Choose reference sequence
Step 4Any specific sequences required
(separated by a new line or a comma):
Step 5Only show exact matches
(e.g. 02:10 will not match 02:100)
Step 6Display mismatches
Step 7Numbering format
Step 8Filter unsequenced alleles
Step 9Output format