Boundaries for FR and CDR regions

[y1zhou]

In IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN, the following bounds were given:

The IMGT unique numbering provides a standardized delimitation of the framework regions (FR1-IMGT: positions 1 to 26, FR2-IMGT: 39 to 55, FR3-IMGT: 66 to 104 and FR4-IMGT: 118 to 128) and of the complementarity determining regions: CDR1-IMGT: 27 to 38, CDR2-IMGT: 56 to 65 and CDR3-IMGT: 105 to 117.

The anchorPointPositions seem to be positions for nucleotide sequences, so the numbers above should be multiplied by 3. These positions still don't seem to match with the bounds given in the code:

mixcr/src/main/resources/parameters/segment_importer_parameters.json

Lines 17 to 46 in 7a85aa6

	"anchorPointPositions": [
	{
	"point": "FR1Begin",
	"position": 0
	},
	{
	"point": "CDR1Begin",
	"position": 78
	},
	{
	"point": "FR2Begin",
	"position": 114
	},
	{
	"point": "CDR2Begin",
	"position": 165
	},
	{
	"point": "FR3Begin",
	"position": 195
	},
	{
	"point": "CDR3Begin",
	"position": 309
	},
	{
	"point": "VEnd",
	"position": "end"
	}
	]

I tested feeding a heavy chain sequence generated from MixCR into ANARCI. the MixCR CDR3 had one additional amino acid on both sides when compared to the ANARCI IMGT-scheme labeled CDR3.

[Alex-Davydov]

Hi,
These parameters are not used, now all coordinates for every species from IMGT are stored in this repository:
https://github.com/repseqio/library-imgt/tree/master/rules (pay attention to 0 based indexing in contrast to IMGT where coordinates start from 1).
Concerning the CDR3 and conservative cysteine and tryptophan / phenylalanine:
The coordinates of frameworks and CDRs in IMGT are determend by protein structure, so the conservative cysteine ​​belongs to FR3 and CDR3 begins after it. But there are situations when 1 or 2 letters are cut off from the cysteine ​​triplet during VDJ recombination, and in order not to lose these sequences, cysteine ​​is included in CDR3 in MiXCR (same for conservative tryptophan / phenylalanine in the J gene).