- 01 Mar, 2016 14 commits
-
-
Mathieu Giraud authored
Many people are used to have the full JUNCTION, including Cys104 and Phe118/Trp118. We thus output both 'cdr3' and 'junction' fields in the json output.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
We compute CDR3startJfull directly from JUNCTIONend.
-
Mathieu Giraud authored
This solves the problem identified in 0aae0cf8.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
- 28 Feb, 2016 17 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
Will be used to test CDR3/JUNCTION detection.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
All full codons aligned with the J germline gene are translated according to this frame.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
Finally Vidjil learns the genetic code.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
This was realized after prototyping and tests by @flothoni. As in IMGT/JunctionAnalysis, the detection relies on the positions of Cys104 and Phe118/Trp118. The detection is here in O(n), taking advantage of the already aligned V and J segments. The current implementation will not give a precise positions when there are insertions or deletions between Cys104 and the end of the V segment (or between the start of J segment and Phe118/Trp118). This could be improved by backtracking the DP matrix.
-
Mathieu Giraud authored
-
- 27 Feb, 2016 9 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
There are currently no gapped J sequences distributed by IMGT. We create these sequences aligned on the Phe118/Trp118.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
The Sequence structure has now an additional field.
-
Mathieu Giraud authored
-