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