When a sequence is quite dissimilar from any germline, the alignment algorithm tends to add gaps here and there to increase similarity with the choosen germline. From 3.24, a post-alignment procedure enables aminoacid rearrangement to make the CDR look like an IMGT CDR, even when the alignment has created gaps in the CDR.
This procedure is enabled by default, and users can modify its configuration before analyzing new sequences. The options are available on the sequence loading page (“Import FASTA” or “Add sequence”).
There exists three levels:
- None: sequences are not rearranged
- IMGT CDR Only: the rearrangement is performed with aminoacids in the IMGT CDR region only
- CDR Extended: the rearrangement is performed in the region used in Kabat numbering.
The following example shows the difference between the 3 levels in the rearrangement of LCDR2:
“CDR Extended” is the equivalent of the procedure used in Kabat numbering and is therefore the default. Note that this option has no effect on Kabat numbering in which “CDR Extended” is always used to conform to Kabat database.