Commit 86d4ef81 authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/user.org: V(D)J designations

parent b5a78e0e
......@@ -306,6 +306,16 @@ the CDR3 is /exactly/ shared by all the reads. The other positions in
the consensus sequence are guaranteed to be present in /at least half/
of the reads. The consensus sequence can thus be shorter than some reads.
** How are computed the V(D)J designations?
In the *built-in Vidjil algorithm*, V(D)J designations are computed /after the clone clustering/ by dynamic programming,
finding the most similar V (or 5') and J (or 3') gene, then trying to match a D gene.
Note that the algorithm also detects some VDDJ or VDDDJ recombinations that may happen in the TRD locus.
Some incomplete or unusual rearrangements (Dh/Jh, Dd2/Dd3, KDE-Intron, mixed TRA-TRD recombinations) are also detected.
Once clones are selected, you can send their sequence to *IMGT/V-QUEST* and *IgBlast*
by clicking on the links just above the sequence view (bottom left).
This opens another window/tab.
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