Artificial gaps in reported amino acid sequences about mixcr HOT 2 CLOSED

Hi, it's hard to tell without looking at the alignment of the specific clone, but I think I know what is going on. So this is a tricky thing. My guess is there are some nucleotide deletions in the sequence. We know that all FRs should end with a complete codon thus should have a strict AA border. If it doesn't, it is not clear where to assign the last AA during the translation. Thats why we translate each FR and CDR from both ends moving towards the center and in a normal scenario this returns an accurate translation. If one nucleotide was deleted or inserted there will be a wrong AA sequence for this region, when exported separately. So this is done in order to correctly define AA borders of the segments ending with a complete codon. The workaround here is to add an export column with the VRegion or the VDJRegion for example. These regions are translated from one end, eliminating the need to distinguish segment borders, and return the correct AA receptor sequence. Use -aaFeature VRegion or -aaFeature VDJRegion for this purpose.

from mixcr.

Ok, thank you!

from mixcr.