Citing IMGT/JunctionAnalysis:
Yousfi Monod, M. et al., Bioinformatics, 20, i379-i385 (2004). PMID: 15262823.
Giudicelli, V., Lefranc, M.-P., Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.prot5634. doi: 10.1101/pdb.prot5634.
PMID: 21632777 Abstract also in IMGT booklet with generous provision from Cold Spring Harbor (CSH) Protocols (high res) (lower res)

IMGT/JunctionAnalysis program version: 2.1.5 (28 July 2015) - IMGT/JunctionAnalysis reference directory release: 201623-2 (7 June 2016)

Analyse the JUNCTION of your IG and TR nucleotide sequences

Sequence sets to test IMGT/JunctionAnalysis are available here

Sequence submission

Type (or copy/paste) your JUNCTION nucleotide sequence(s) into the box below (click here for required format):
Or give the path access to a local file containing your sequences:
Click here for an example of IMGT/JunctionAnalysis results.

Display results

List of all eligible D-GENE: Yes No
Colored IMGT AA classes and histogram: Yes No
Output order: Same order as input
CDR3-IMGT length decreasing order
CDR3-IMGT length increasing order

Advanced parameters

5' and 3' ends of the JUNCTION: Default
May start and/or end with any codon
Number of D-GENEs (for IGH, TRB and TRD JUNCTION):
Number of accepted mutations: in 3'V-REGION
Delimitation of 3'V-REGION, D-REGION and 5'J-REGION: Default
Stop trimming with the first encountered identical nucleotide
D-GENE choice (if several have the same score): The less mutated one
The longest one
The one more upstream in the locus