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Release of MixMHC2pred-2.0.
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jracle85 committed Oct 3, 2022
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2 changes: 1 addition & 1 deletion Alleles_list.txt
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List of alleles available in MixMHC2pred v2.0.RC
List of alleles available in MixMHC2pred v2.0
AlleleName OfficialName
DRB1_01_01 HLA-DRB1*01:01
DRB1_01_02 HLA-DRB1*01:02
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6 changes: 4 additions & 2 deletions FAQ.md
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Expand Up @@ -49,7 +49,7 @@ scores.
## Can I use MixMHC2pred for commercial purposes

If you plan to use MixMHC2pred for commercial purposes, you are required to
obtain a separate license. To do so, please contact <eauffarth@licr.org>
obtain a separate license. To do so, please contact <nbulgin@lcr.org>
at the Ludwig Institute for Cancer Research Ltd.

## Who should I contact in case of a technical or other issue
Expand All @@ -62,7 +62,9 @@ that is causing the issue.

If you are using MixMHC2pred, please refer to

Racle, J., et al., Accurate predictions of MHC-II specificities (in prep.).
Racle, J., et al., Machine learning predictions of MHC-II specificities reveal
alternative binding mode of class II epitopes. *bioRxiv* (2022)
(available [here](https://doi.org/10.1101/2022.06.26.497561)).

and

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8 changes: 8 additions & 0 deletions NEWS
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Release notes from MixMHC2pred
========================================================================

Version 2.0 (03.10.2022)
------------------------------------------------------------------------
* Release of MixMHC2pred-v2.0 (as full version, not RC version anymore).
* No major change with respect to the 2.0.RC (see news of 10.06.2022). It was
only retrained after minor changes on the training data used.


Version 2.0.RC (10.06.2022)
------------------------------------------------------------------------
* Major update of MixMHC2pred, allowing for pan-allele predictions for human and
non-human MHC-II alleles.
* Implementation vastly changed; it is now based on multiple neural networks and
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18 changes: 9 additions & 9 deletions PWMdef/BoLA_DRB3_001_01.txt
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Expand Up @@ -35,13 +35,13 @@ W 0.0825 0.0435 0.6387 0.0389 0.2474 0.0383 1.3904 0.0759 1.2142
Y 0.5871 1.1289 3.3362 0.0892 0.6191 0.0797 1.6228 1.0304 1.0469

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
12 99.5307 0.083 0.1488 0 0.3949 0.3733
13 98.9574 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3293 0.0043 0.0259 0.161 0 0.4702 0.2976 0.0409
15 98.0138 0.0017 0.0096 0.0839 0.3761 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.522 0.1562 0.0472 0.0079
17 98.7349 8e-04 0.0019 0.0146 0.1152 0.4294 0.2806 0.114 0.0362 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
19 99.5134 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2917 0.1843 0.0762 0.0263 0.0055
20 99.6911 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2453 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1384 0.2552 0.2215 0.1327 0.043 0.0166 0.0041
58 changes: 29 additions & 29 deletions PWMdef/BoLA_DRB3_001_03.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -13,35 +13,35 @@ pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1465 1.4655 1.6064 3.2247 0.7226 0.6129 1.2577 1.1812 0.194
C 0.0713 0.1005 0.1842 0.1696 0.088 0.102 0.2619 0.116 0.0546
D 0.0594 0.6538 0.2739 1.0039 0.8378 0.5374 0.5804 0.5499 0.0818
E 0.047 1.7354 0.6463 0.173 1.2419 0.3235 1.2669 0.9164 0.1446
F 1.8604 0.7927 1.3955 0.8709 0.4796 0.1725 0.9863 0.6052 0.7831
G 0.0707 0.46 0.5172 0.502 0.6401 0.1693 0.8959 0.9468 0.1863
H 0.0614 1.5931 1.0273 3.7008 1.3412 1.589 1.1646 1.5282 0.1647
I 7.2072 0.9289 2.1104 0.606 1.4051 1.5996 0.9942 1.0162 0.2735
K 0.0495 1.1939 0.9458 0.1554 2.289 4.498 0.9144 1.5537 9.2261
L 2.9731 0.6749 0.8213 0.1882 1.0476 0.8571 1.4551 1.0855 0.3493
M 1.3263 0.4812 1.171 0.1542 0.7469 0.514 0.9297 0.5538 0.578
N 0.0484 1.3847 0.7754 1.369 0.7344 0.7587 1.5932 0.9038 0.151
P 0.1101 0.0719 1.1215 0.1192 0.5616 0.3364 0.6369 1.2759 0.039
Q 0.0497 1.2558 1.0606 0.2154 1.1306 0.6616 0.9695 1.0813 0.163
R 0.0436 1.2263 0.663 0.1 1.3004 2.9351 0.6964 1.4304 4.3748
S 0.0441 0.96 0.9522 2.416 0.4621 0.2675 0.7842 0.746 0.1195
T 0.1397 1.4589 0.6026 1.9738 1.0057 0.8711 0.7388 0.863 0.1106
V 3.7624 1.2283 1.3626 1.7616 1.7657 1.6845 1.0993 0.997 0.3469
W 0.4394 0.3642 0.9519 0.199 0.3143 0.1182 0.8476 0.3334 0.6464
Y 0.6058 1.2166 2.6351 0.1474 0.7234 0.176 1.4858 1.0766 1.0786
A 0.1365 1.3819 1.5882 3.5767 0.7724 0.5504 1.2653 1.1786 0.1883
C 0.0653 0.0859 0.2204 0.1134 0.089 0.1093 0.2178 0.1131 0.0638
D 0.0499 0.6727 0.2955 0.926 0.8698 0.4339 0.5004 0.5371 0.0704
E 0.0392 1.7044 0.6706 0.1566 1.194 0.323 1.3295 0.9166 0.1504
F 1.8481 0.8393 1.3697 0.7327 0.4673 0.1684 0.8422 0.6046 0.7524
G 0.0694 0.4529 0.5366 0.4375 0.6668 0.155 0.8755 0.9621 0.1596
H 0.0568 1.6694 1.0181 3.4838 1.284 1.655 1.1246 1.5437 0.1307
I 7.3492 0.9773 2.0981 0.6311 1.3298 1.64 1.0509 1.0119 0.245
K 0.0424 1.1873 0.9788 0.1377 2.3543 4.8406 0.8729 1.5625 9.4292
L 3.1314 0.683 0.8298 0.1395 1.0405 0.7882 1.5193 1.0918 0.3385
M 1.2268 0.4878 1.2127 0.1304 0.7106 0.4759 0.8646 0.5453 0.5353
N 0.0487 1.3314 0.7867 1.1385 0.7376 0.6991 1.8327 0.8962 0.1007
P 0.1002 0.0706 1.1034 0.1146 0.6168 0.321 0.6918 1.2711 0.037
Q 0.0426 1.3149 1.0122 0.1772 1.1014 0.6957 1.0762 1.0865 0.1487
R 0.0389 1.2296 0.6748 0.0772 1.2854 2.9545 0.6401 1.4361 4.4694
S 0.0403 0.9684 0.9167 2.5695 0.4964 0.226 0.7784 0.7431 0.0933
T 0.1459 1.4653 0.5642 1.9009 1.0048 0.8402 0.7019 0.862 0.1077
V 3.5629 1.1942 1.3979 1.8576 1.688 1.6869 1.0773 0.984 0.3331
W 0.4113 0.4664 0.914 0.1606 0.2962 0.1227 0.7006 0.333 0.7594
Y 0.4869 1.2296 2.6447 0.1171 0.7353 0.1772 1.252 1.0692 0.8731

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
12 99.5307 0.083 0.1488 0 0.3949 0.3733
13 98.9574 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3293 0.0043 0.0259 0.161 0 0.4702 0.2976 0.0409
15 98.0138 0.0017 0.0096 0.0839 0.3761 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.522 0.1562 0.0472 0.0079
17 98.7349 8e-04 0.0019 0.0146 0.1152 0.4294 0.2806 0.114 0.0362 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
19 99.5134 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2917 0.1843 0.0762 0.0263 0.0055
20 99.6911 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2453 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1384 0.2552 0.2215 0.1327 0.043 0.0166 0.0041
58 changes: 29 additions & 29 deletions PWMdef/BoLA_DRB3_002_01.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -13,35 +13,35 @@ pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1391 0.9786 1.5907 0.5882 1.0627 0.3353 1.0604 1.1812 1.092
C 0.0583 0.1182 0.2804 0.1561 0.1722 0.0273 0.28 0.116 0.542
D 0.0402 0.5555 0.5111 0.3207 1.3732 0.2206 0.9503 0.5499 0.1885
E 0.0321 1.1065 0.795 0.3496 1.1806 0.2015 1.3143 0.9164 0.2375
F 0.8712 0.8442 1.0454 4.8675 0.4956 0.0511 0.9596 0.6052 1.4774
G 0.0626 0.3341 0.7087 0.1811 0.7015 0.1031 0.8136 0.9468 0.4496
H 0.041 1.4506 0.8247 2.3532 1.2293 1.1755 1.34 1.5282 0.3514
I 8.7661 1.5874 2.3246 1.4751 0.9375 0.5336 1.2289 1.0162 1.9125
K 0.0339 1.7251 0.8812 0.7418 1.7439 8.5146 0.8889 1.5537 0.212
L 2.7494 0.856 0.9193 0.8987 0.4537 0.2268 0.8165 1.0855 2.2623
M 1.3964 0.5286 1.1058 1.3633 0.634 0.1342 1.0087 0.5538 1.4762
N 0.0398 1.0179 0.8488 1.1157 1.1752 0.253 1.9542 0.9038 0.6783
P 0.0759 0.0529 1.0026 0.0635 1.1399 0.1812 0.7904 1.2759 0.1227
Q 0.0349 1.1967 0.8584 0.7749 1.2348 0.3052 1.2106 1.0813 0.55
R 0.0305 1.746 0.7923 0.6435 1.1435 4.645 0.6144 1.4304 0.375
S 0.033 0.7128 0.7845 0.2884 0.9813 0.1256 0.8682 0.746 0.6773
T 0.1218 1.1169 0.8781 0.4386 1.3604 0.4821 0.8502 0.863 0.8719
V 3.9808 1.9381 1.4068 1.0444 0.8719 0.5979 1.1176 0.997 3.0834
W 0.1798 0.5113 0.5362 5.8232 0.3946 0.0396 0.8161 0.3334 0.2168
Y 0.1653 1.1473 1.7551 5.5436 0.9295 0.0692 1.5865 1.0766 2.7968
A 0.1329 0.971 1.5602 0.5787 1.0353 0.2728 1.0787 1.1786 1.0957
C 0.0539 0.118 0.3027 0.17 0.1567 0.0277 0.3367 0.1131 0.5635
D 0.0395 0.5546 0.4931 0.3449 1.303 0.1836 0.8888 0.5371 0.1935
E 0.0275 1.1045 0.8117 0.3395 1.1565 0.1973 1.3281 0.9166 0.2099
F 0.8949 0.8507 1.0192 5.104 0.5045 0.049 0.8386 0.6046 1.543
G 0.0598 0.3361 0.6765 0.1806 0.7345 0.0881 0.8986 0.9621 0.438
H 0.0379 1.4432 0.8006 2.4459 1.2492 1.2944 1.3559 1.5437 0.3602
I 8.7578 1.5947 2.3123 1.7167 0.9248 0.5053 1.2913 1.0119 1.9572
K 0.0307 1.7443 0.8895 0.6058 1.8041 8.6106 0.924 1.5625 0.194
L 2.9065 0.8388 0.9232 0.8361 0.4894 0.2176 0.8812 1.0918 2.2274
M 1.2553 0.5271 1.1039 1.1885 0.6076 0.1238 1.0001 0.5453 1.4793
N 0.0347 1.0223 0.8403 1.0478 1.1801 0.2155 2.0522 0.8962 0.8272
P 0.0794 0.0548 1.0128 0.0773 1.1403 0.1729 0.7539 1.2711 0.1121
Q 0.0298 1.2417 0.8582 0.7737 1.2549 0.3081 1.2097 1.0865 0.5299
R 0.0294 1.734 0.8133 0.5737 1.1387 4.7015 0.6236 1.4361 0.2936
S 0.0298 0.7046 0.806 0.319 0.9356 0.1131 0.8059 0.7431 0.6567
T 0.1199 1.109 0.8623 0.4321 1.3668 0.5015 0.8045 0.862 0.8387
V 3.8187 1.94 1.4503 1.1344 0.8879 0.5931 1.0833 0.984 3.1594
W 0.1738 0.5062 0.5576 5.4484 0.4484 0.0417 0.8203 0.333 0.1929
Y 0.1263 1.153 1.7284 5.5051 0.9104 0.07 1.3926 1.0692 2.8655

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
12 99.5307 0.083 0.1488 0 0.3949 0.3733
13 98.9574 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3293 0.0043 0.0259 0.161 0 0.4702 0.2976 0.0409
15 98.0138 0.0017 0.0096 0.0839 0.3761 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.522 0.1562 0.0472 0.0079
17 98.7349 8e-04 0.0019 0.0146 0.1152 0.4294 0.2806 0.114 0.0362 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
19 99.5134 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2917 0.1843 0.0762 0.0263 0.0055
20 99.6911 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2453 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1384 0.2552 0.2215 0.1327 0.043 0.0166 0.0041
58 changes: 29 additions & 29 deletions PWMdef/BoLA_DRB3_002_02.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,35 +13,35 @@ pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1391 0.9786 1.5907 0.5882 1.0627 0.3353 1.0604 1.1812 1.092
C 0.0583 0.1182 0.2804 0.1561 0.1722 0.0273 0.28 0.116 0.542
D 0.0402 0.5555 0.5111 0.3207 1.3732 0.2206 0.9503 0.5499 0.1885
E 0.0321 1.1065 0.795 0.3496 1.1806 0.2015 1.3143 0.9164 0.2375
F 0.8712 0.8442 1.0454 4.8675 0.4956 0.0511 0.9596 0.6052 1.4774
G 0.0626 0.3341 0.7087 0.1811 0.7015 0.1031 0.8136 0.9468 0.4496
H 0.041 1.4506 0.8247 2.3532 1.2293 1.1755 1.34 1.5282 0.3514
I 8.7661 1.5874 2.3246 1.4751 0.9375 0.5336 1.2289 1.0162 1.9125
K 0.0339 1.7251 0.8812 0.7418 1.7439 8.5146 0.8889 1.5537 0.212
L 2.7494 0.856 0.9193 0.8987 0.4537 0.2268 0.8165 1.0855 2.2623
M 1.3964 0.5286 1.1058 1.3633 0.634 0.1342 1.0087 0.5538 1.4762
N 0.0398 1.0179 0.8488 1.1157 1.1752 0.253 1.9542 0.9038 0.6783
P 0.0759 0.0529 1.0026 0.0635 1.1399 0.1812 0.7904 1.2759 0.1227
Q 0.0349 1.1967 0.8584 0.7749 1.2348 0.3052 1.2106 1.0813 0.55
R 0.0305 1.746 0.7923 0.6435 1.1435 4.645 0.6144 1.4304 0.375
S 0.033 0.7128 0.7845 0.2884 0.9813 0.1256 0.8682 0.746 0.6773
T 0.1218 1.1169 0.8781 0.4386 1.3604 0.4821 0.8502 0.863 0.8719
V 3.9808 1.9381 1.4068 1.0444 0.8719 0.5979 1.1176 0.997 3.0834
W 0.1798 0.5113 0.5362 5.8232 0.3946 0.0396 0.8161 0.3334 0.2168
Y 0.1653 1.1473 1.7551 5.5436 0.9295 0.0692 1.5865 1.0766 2.7968
A 0.1329 0.971 1.5602 0.5787 1.0353 0.2728 1.0787 1.1786 1.0957
C 0.0539 0.118 0.3027 0.17 0.1567 0.0277 0.3367 0.1131 0.5635
D 0.0395 0.5546 0.4931 0.3449 1.303 0.1836 0.8888 0.5371 0.1935
E 0.0275 1.1045 0.8117 0.3395 1.1565 0.1973 1.3281 0.9166 0.2099
F 0.8949 0.8507 1.0192 5.104 0.5045 0.049 0.8386 0.6046 1.543
G 0.0598 0.3361 0.6765 0.1806 0.7345 0.0881 0.8986 0.9621 0.438
H 0.0379 1.4432 0.8006 2.4459 1.2492 1.2944 1.3559 1.5437 0.3602
I 8.7578 1.5947 2.3123 1.7167 0.9248 0.5053 1.2913 1.0119 1.9572
K 0.0307 1.7443 0.8895 0.6058 1.8041 8.6106 0.924 1.5625 0.194
L 2.9065 0.8388 0.9232 0.8361 0.4894 0.2176 0.8812 1.0918 2.2274
M 1.2553 0.5271 1.1039 1.1885 0.6076 0.1238 1.0001 0.5453 1.4793
N 0.0347 1.0223 0.8403 1.0478 1.1801 0.2155 2.0522 0.8962 0.8272
P 0.0794 0.0548 1.0128 0.0773 1.1403 0.1729 0.7539 1.2711 0.1121
Q 0.0298 1.2417 0.8582 0.7737 1.2549 0.3081 1.2097 1.0865 0.5299
R 0.0294 1.734 0.8133 0.5737 1.1387 4.7015 0.6236 1.4361 0.2936
S 0.0298 0.7046 0.806 0.319 0.9356 0.1131 0.8059 0.7431 0.6567
T 0.1199 1.109 0.8623 0.4321 1.3668 0.5015 0.8045 0.862 0.8387
V 3.8187 1.94 1.4503 1.1344 0.8879 0.5931 1.0833 0.984 3.1594
W 0.1738 0.5062 0.5576 5.4484 0.4484 0.0417 0.8203 0.333 0.1929
Y 0.1263 1.153 1.7284 5.5051 0.9104 0.07 1.3926 1.0692 2.8655

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
12 99.5307 0.083 0.1488 0 0.3949 0.3733
13 98.9574 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3293 0.0043 0.0259 0.161 0 0.4702 0.2976 0.0409
15 98.0138 0.0017 0.0096 0.0839 0.3761 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.522 0.1562 0.0472 0.0079
17 98.7349 8e-04 0.0019 0.0146 0.1152 0.4294 0.2806 0.114 0.0362 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
19 99.5134 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2917 0.1843 0.0762 0.0263 0.0055
20 99.6911 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2453 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1384 0.2552 0.2215 0.1327 0.043 0.0166 0.0041
58 changes: 29 additions & 29 deletions PWMdef/BoLA_DRB3_003_01.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,35 +13,35 @@ pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.0934 0.9786 1.4683 1.1293 0.9304 2.5989 0.9289 1.1812 0.9352
C 0.049 0.1182 0.3474 0.2577 0.2937 0.2749 0.181 0.116 0.5129
D 0.0361 0.5555 0.4121 1.9061 1.0494 0.513 0.9071 0.5499 0.2342
E 0.0576 1.1065 0.6688 0.7839 1.0349 0.8162 1.2776 0.9164 0.2369
F 8.2964 0.8442 1.1583 0.3547 0.6803 0.4056 0.469 0.6052 1.1142
G 0.0619 0.3341 0.6012 0.7662 0.9066 1.2411 0.9229 0.9468 0.3379
H 0.1244 1.4506 0.8028 0.4577 1.3764 0.3803 0.9597 1.5282 0.3055
I 2.7704 1.5874 2.2495 0.6114 0.88 1.4893 1.2378 1.0162 1.8667
K 0.0618 1.7251 0.9267 0.2101 1.573 0.0999 0.5508 1.5537 0.2538
L 1.3527 0.856 0.9042 0.4972 0.6022 0.7256 0.7632 1.0855 2.5009
M 0.9209 0.5286 1.3498 0.5831 0.8672 0.5703 0.4483 0.5538 1.4184
N 0.0713 1.0179 0.915 8.7352 1.2193 1.9808 2.7384 0.9038 0.9454
P 0.0388 0.0529 1.1054 0.1232 1.4207 1.3218 1.6597 1.2759 0.1017
Q 0.0536 1.1967 0.9109 1.1762 1.1273 1.3504 1.3531 1.0813 0.4646
R 0.0379 1.746 0.8265 0.1932 1.1305 0.1 0.4304 1.4304 0.4499
S 0.0414 0.7128 0.8742 1.1615 0.9185 0.7966 0.7061 0.746 0.6047
T 0.0773 1.1169 0.8169 0.9636 1.2222 1.1279 1.1622 0.863 0.8281
V 0.9818 1.9381 1.4084 0.7256 0.8829 1.8376 1.358 0.997 3.2316
W 4.5203 0.5113 0.748 0.2846 0.6652 0.0888 0.4495 0.3334 0.2579
Y 10.5593 1.1473 1.7927 0.2256 0.8134 0.213 0.8112 1.0766 2.7484
A 0.0896 0.971 1.4815 1.2757 0.9073 2.2001 0.9974 1.1786 0.915
C 0.0511 0.118 0.3191 0.2406 0.2442 0.3249 0.1454 0.1131 0.543
D 0.0347 0.5546 0.4037 2.0286 1.1017 0.4103 0.8599 0.5371 0.2503
E 0.0549 1.1045 0.6979 0.8395 1.1392 0.5803 1.4225 0.9166 0.2137
F 8.5177 0.8507 1.0737 0.4559 0.6491 0.5897 0.4141 0.6046 1.2217
G 0.0609 0.3361 0.5972 0.7464 0.969 0.9841 0.921 0.9621 0.3201
H 0.1257 1.4432 0.7858 0.4779 1.478 0.5154 0.8491 1.5437 0.304
I 2.7942 1.5947 2.2462 0.5977 0.8037 2.2073 1.1836 1.0119 2.0243
K 0.0562 1.7443 0.9462 0.2381 1.684 0.146 0.5156 1.5625 0.2238
L 1.3764 0.8388 0.9202 0.431 0.6275 1.1508 0.7226 1.0918 2.3908
M 0.9048 0.5271 1.333 0.6021 0.6395 0.7988 0.3719 0.5453 1.5276
N 0.0706 1.0223 0.8979 7.766 1.2517 1.5466 2.9094 0.8962 1.0995
P 0.0383 0.0548 1.1284 0.1116 1.3613 1.2013 1.761 1.2711 0.0948
Q 0.0511 1.2417 0.8793 1.3875 1.2446 1.2948 1.3806 1.0865 0.4907
R 0.0397 1.734 0.8779 0.2282 1.0887 0.1471 0.3725 1.4361 0.3231
S 0.0409 0.7046 0.8629 1.2213 0.8592 0.6227 0.7627 0.7431 0.5786
T 0.0763 1.109 0.7902 0.8886 1.1694 0.9824 1.1135 0.862 0.7815
V 0.9921 1.94 1.4579 0.7643 0.8393 2.0785 1.2967 0.984 3.3741
W 4.4804 0.5062 0.5861 0.3893 0.558 0.1948 0.3337 0.333 0.2352
Y 10.1766 1.153 1.744 0.2837 0.7207 0.3881 0.6278 1.0692 2.7313

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
12 99.5307 0.083 0.1488 0 0.3949 0.3733
13 98.9574 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3293 0.0043 0.0259 0.161 0 0.4702 0.2976 0.0409
15 98.0138 0.0017 0.0096 0.0839 0.3761 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.522 0.1562 0.0472 0.0079
17 98.7349 8e-04 0.0019 0.0146 0.1152 0.4294 0.2806 0.114 0.0362 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
19 99.5134 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2917 0.1843 0.0762 0.0263 0.0055
20 99.6911 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2453 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1384 0.2552 0.2215 0.1327 0.043 0.0166 0.0041
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