Mikhail Shugay
Mikhail Shugay
Thank you for this submission. I've added the paper label (only repository admins can do that) and edited your comment to add a link to the paper. We'll make a...
Hi! 1) Yes, its the correct way 2) Correct 3) They say ``A standard cutoff of .5% specific cytotoxicity was used to define positive clones. In all assays, this was...
The species list is hard-coded, I can change it. I think we have several V/J segments for Bos, don't know if it is possible to check CDR3 sequences. As noted...
Looks like I've missed that. C/F issue is not a problem, as this is human we just add them (mice have C/W in some J if I remember it correctly)....
1. One can try to perform a frequency-based pairing, i.e. top TRB and TRA are likely to be paired if they are of approx. the same frequency. Better to put...
I've just discovered extremely strange artefacts - cysteines inside CDR3, strange J alignments. Downloaded raw data and re-analyzing it. Should replace the chunk soon (except for paired sequences)..
No problems, I've also missed this, quite hard to check all 10k sequences :)
After checking, it looks like those Cys codons are mostly in N-region of TRA CDR3s, so perhaps they are real. They have quite low frequency (
You can ask Paul Thomas, but I think these sequences are in his latest Nature paper (that is already here) in C-F format
Isn't it in Table1 at the top?