Commit 526beeb8 authored by Mikael Salson's avatar Mikael Salson

germline: changes in IMGT germlines

Changes in IGHV:
1. Three new genes (IGHV3-23D*02, IGHV3-30-5*01 and
   IGHV3-30-5*02). Welcome on board.
2. One gene deleted (IGHV4-28*05). You left us too early,
   we had good time together…
3. One gene (IGHV3-30-3*01) increased by two nucleotides. Congratulations!

Functionality changes in two genes in IGLV (IGLV10-54*03) and TRAV
(TRAV11*01).
parent 4d6c3ae6
......@@ -4,13 +4,13 @@
$ Check md5 in germline/, sequences split from IMGT
1:3a655c9d99ca04907a120f1b69febf2e IGHD.fa
1:0d87f672c582e7e15cdcaa0fb5e08f6f IGHJ.fa
1:4f43acd99f6285d3039e2626ed753c8a IGHV.fa
1:b59eb57893dbab69d98eb712722bf603 IGHV.fa
1:6a696e7cc21b8ffb7e3adbcf37167711 IGKJ.fa
1:2746f12c8af2a9b42b166ef468dd08d9 IGKV.fa
1:a6bdc2aa82d151e30d10d302559355b6 IGLJ.fa
1:6012b3ce22ce0a669ba1b8e670bd2db1 IGLV.fa
1:3184a810b22ff5557e99f99906c92fef IGLV.fa
1:17513843a8d4d2025c38afa13249e2e1 TRAJ.fa
1:eda2b0f8e711fd6d4cfb0bcdf166da90 TRAV.fa
1:a7eedfb8feda1107884ad9a363c90831 TRAV.fa
1:f66c70cda5b369aecd34ab1cd11e7415 TRBD.fa
1:cc20222cdb7a381ff5a34030bee91e08 TRBJ.fa
1:5751f4aea01aebe77575f27d0150a8f2 TRBV.fa
......
!LAUNCH: ../../vidjil -e 10 -z 0 -V ../../germline/IGHV.fa -D ../../germline/IGHD.fa -J ../../germline/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# ../../data/Stanford_S22.fasta
$ Parses IGHV.fa germline
1: 101627 bp in 348 sequences
1: 102221 bp in 350 sequences
$ Parses IGHD.fa germline
1: 1070 bp in 44 sequences
......
DATA=???[VDJ].fa IGK-INTRON.fa IGK-KDE.fa TRDD2_upstream.fa TRDD3_downstream.fa ???[VDJ]_upstream.fa ???[VDJ]_downstream.fa
DATA=???[VDJ].fa IGK-INTRON.fa IGK-KDE.fa TRDD2_upstream.fa TRDD3_downstream.fa ???[VDJ]_upstream.fa ???[VDJ]_downstream.fa {IG,TR}*=*.fa
germline:
sh get-saved-germline
......
28
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30
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