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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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symbol meaning in CDR3? #64

Closed swuecho closed 8 years ago

swuecho commented 8 years ago

I find '*', '~', '-' in CDR3, what does each of them means? Thanks.

dbolotin commented 8 years ago

* - stop codon ~ - incomplete codon (it is a very old syntax, now the _ symbol is used instead) Here is an example of translation of the following nucleotide sequence: ATTAGACA

ATT AG  ACA
 I   _   T    -   current syntax
 I   ~   T    -   old syntax

- - should never appear in CDR3 sequences (could you provide an example?)

What version of MiXCR do you use?

swuecho commented 8 years ago

Yeah. I should type '_' instead of '-'.

'~' was found from result of mitcr.

Thanks.