Commit f9403618 authored by Mikaël Salson's avatar Mikaël Salson

homo-sapiens.g: Use downstream sequence for the J gene

When the J gene is too deleted we may not have enough signal.
This should help recognizing more J recombinations. See #3008.

(edited by @magiraud following 928c7390)
parent 118645eb
......@@ -14,7 +14,7 @@
"description": "Human T-cell receptor, alpha locus (14q11.2)",
"recombinations": [ {
"5": ["TRAV.fa"],
"3": ["TRAJ.fa"]
"3": ["TRAJ+down.fa"]
} ],
"parameters": {
"seed": "13s"
......@@ -28,7 +28,7 @@
"recombinations": [ {
"5": ["TRBV.fa"],
"4": ["TRBD.fa"],
"3": ["TRBJ.fa"]
"3": ["TRBJ+down.fa"]
} ],
"parameters": {
"seed": "12s"
......@@ -41,7 +41,7 @@
"follows": "TRB",
"recombinations": [ {
"5": ["TRBD+up.fa"],
"3": ["TRBJ.fa"]
"3": ["TRBJ+down.fa"]
} ],
"parameters": {
"seed": "12s"
......@@ -54,7 +54,7 @@
"description": "Human T-cell receptor, gamma locus (7p14)",
"recombinations": [ {
"5": ["TRGV.fa"],
"3": ["TRGJ.fa"]
"3": ["TRGJ+down.fa"]
} ],
"parameters": {
"seed": "10s"
......@@ -68,7 +68,7 @@
"recombinations": [ {
"5": ["TRDV.fa"],
"4": ["TRDD.fa"],
"3": ["TRDJ.fa"]
"3": ["TRDJ+down.fa"]
} ],
"parameters": {
"seed": "10s"
......@@ -81,10 +81,10 @@
"recombinations": [ {
"5": ["TRDV.fa"],
"4": ["TRDD.fa"],
"3": ["TRAJ.fa"]
"3": ["TRAJ+down.fa"]
}, {
"5": ["TRDD+up.fa"],
"3": ["TRAJ.fa"]
"3": ["TRAJ+down.fa"]
} ],
"parameters": {
"seed": "13s"
......@@ -101,7 +101,7 @@
}, {
"5": ["TRDD2+up.fa"],
"4": ["TRDD.fa"],
"3": ["TRDJ.fa"]
"3": ["TRDJ+down.fa"]
}, {
"5": ["TRDD2+up.fa"],
"3": ["TRDD3+down.fa"]
......@@ -118,7 +118,7 @@
"recombinations": [ {
"5": ["IGHV.fa"],
"4": ["IGHD.fa"],
"3": ["IGHJ.fa"]
"3": ["IGHJ+down.fa"]
} ],
"parameters": {
"seed": "12s"
......@@ -131,7 +131,7 @@
"follows": "IGH",
"recombinations": [ {
"5": ["IGHD+up.fa"],
"3": ["IGHJ.fa"]
"3": ["IGHJ+down.fa"]
} ],
"parameters": {
"seed": "12s"
......@@ -144,7 +144,7 @@
"description": "Human immunoglobulin, kappa locus (2p11.2)",
"recombinations": [ {
"5": ["IGKV.fa"],
"3": ["IGKJ.fa"]
"3": ["IGKJ+down.fa"]
} ],
"parameters": {
"seed": "10s"
......@@ -170,7 +170,7 @@
"description": "Human immunoglobulin, lambda locus (22q11.2)",
"recombinations": [ {
"5": ["IGLV.fa"],
"3": ["IGLJ.fa"]
"3": ["IGLJ+down.fa"]
} ],
"parameters": {
"seed": "10s"
......
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