Automated reassembly of TCR sequence from VDJ alleles + CDR3?


#1

Hi all,

I’ve been looking for an automated way to reassemble the complete TCR sequence from the output files of VDJ analysis tools. I can’t seem to find anything that does this after looking at IEDB and at Mikhail Shugay’s post on software here, and at https://omictools.com/rep-seq-category.

Does anyone know of a tool that can do this?

Ed


#2

The CreateGermlines tool in Change-O does this. Assuming there is sufficient information about the alignment in the input data.


#3

not sure it’s quite what I’m looking for, but it’s the closest yet - Thanks javh!


#4

In case you don’t find any ready solution here is how to do it manually, assuming that you have

then the full sequence will be (pseudocode in java)

vSeq.substring(0, vRef - 3) + cdr3Seq + jSeq.substring(jRef + 4)

Hope I haven’t messed the indices : )

The missing things are the UTR of V segment (you can try to fetch them from e.g. UCSC genome browser) and constant region. As for the constant region, its not resolved in most of the sequencing protocols.


#5

Thanks Mikhail, the compound file really helped solve this simply


#6

For expression purposes, I built on Mikhail’s response by downloading from IMGT the sequence for the 5’UTRs, as well as the L1-V exon region, as described in this FAQ on the IMGT website:
http://www.imgt.org/FAQ/#question32

Hope this helps someone else clone interesting TCRs