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Commit e86e4bf6 by Mustafa Tekpinar
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Added introduction.rst and more documentation.

parent 42dbf51a
Showing with 1049 additions and 467 deletions
data/BLAT_jet.res
AA pos chain axs cv pc tr freq trace clusters clusnumber ssjetormax
MET 1 A 1.0 0.1798 0.6606 0.0 0.0 0.0 0.0 0.0 0.0
SER 2 A 1.0 0.4007 0.3574 0.0 0.0 0.0 0.0 0.0 0.0
ILE 3 A 1.0 0.4642 0.638 0.0 0.0 0.0 0.0 0.0 0.0
GLN 4 A 1.0 0.5616 0.4343 0.0971 0.18 0.0174 0.0 0.0 0.0174
HIS 5 A 1.0 0.6781 0.5972 0.1113 0.06 0.0066 0.0 0.0 0.0066
PHE 6 A 1.0 0.645 1.0 0.0928 0.12 0.0111 0.0 0.0 0.0111
ARG 7 A 1.0 0.6488 0.5067 0.1249 0.34 0.0424 0.0 0.0 0.0424
VAL 8 A 1.0 0.7859 0.5656 0.1094 0.54 0.059 0.0 0.0 0.059
ALA 9 A 1.0 0.8354 0.3846 0.1142 0.52 0.0594 0.0 0.0 0.0594
LEU 10 A 1.0 0.7349 0.7058 0.1591 0.14 0.0222 0.0 0.0 0.0222
ILE 11 A 1.0 0.7358 0.638 0.1536 0.4 0.0614 0.0 0.0 0.0614
PRO 12 A 1.0 0.7525 0.466 0.1143 0.38 0.0434 0.0 0.0 0.0434
PHE 13 A 1.0 0.7142 1.0 0.1342 0.78 0.1047 0.0 0.0 0.1047
PHE 14 A 1.0 0.686 1.0 0.1743 0.3 0.0522 0.0 0.0 0.0522
ALA 15 A 1.0 0.8723 0.3846 0.21 0.7 0.147 0.0 0.0 0.147
ALA 16 A 1.0 0.8165 0.3846 0.3606 0.34 0.1226 0.0 0.0 0.1226
PHE 17 A 1.0 0.7198 1.0 0.2187 0.76 0.1662 0.0 0.0 0.1662
CYS 18 A 1.0 0.7581 0.6425 0.2452 0.7 0.1716 0.0 0.0 0.1716
LEU 19 A 1.0 0.7318 0.7058 0.2104 0.94 0.1978 0.0 0.0 0.1978
PRO 20 A 1.0 0.6357 0.466 0.2601 0.74 0.1925 0.0 0.0 0.1925
VAL 21 A 1.0 0.6017 0.5656 0.2712 0.54 0.1464 0.0 0.0 0.1464
PHE 22 A 1.0 0.491 1.0 0.2798 0.52 0.1455 0.0 0.0 0.1455
ALA 23 A 1.0 0.4599 0.3846 0.3037 0.92 0.2794 0.0 0.0 0.2794
HIS 24 A 1.0 0.4471 0.5972 0.2954 0.68 0.2009 0.0 0.0 0.2009
PRO 25 A 1.0 0.4918 0.466 0.2696 0.9 0.2426 0.0 0.0 0.2426
GLU 26 A 1.0 0.4252 0.3348 0.3842 0.66 0.2536 0.0 0.0 0.38
THR 27 A 1.0 0.5993 0.3257 0.5596 1.0 0.5596 0.0 0.0 0.5794
LEU 28 A 1.0 0.5513 0.7058 0.3062 0.86 0.2633 0.0 0.0 0.6285
VAL 29 A 1.0 0.443 0.5656 0.2447 0.82 0.2006 0.0 0.0 0.5043
LYS 30 A 1.0 0.5102 0.2488 0.3921 0.9 0.3528 0.0 0.0 0.4315
VAL 31 A 0.5 0.6384 0.5656 0.6009 0.98 0.5889 0.0 0.0 0.6136
LYS 32 A 1.0 0.4541 0.2488 0.4482 0.88 0.3944 0.0 0.0 0.4242
ASP 33 A 1.0 0.4253 0.3212 0.4874 0.72 0.3509 0.0 0.0 0.3881
ALA 34 A 0.8 0.5623 0.3846 0.6821 1.0 0.6821 0.0 0.0 0.6222
GLU 35 A 1.0 0.4961 0.3348 0.7952 1.0 0.7952 0.0 0.0 0.6457
ASP 36 A 1.0 0.3478 0.3212 0.3964 0.82 0.325 0.0 0.0 0.3364
GLN 37 A 1.0 0.357 0.4343 0.3527 0.92 0.3244 0.0 0.0 0.3956
LEU 38 A 0.8 0.5159 0.7058 0.5341 1.0 0.5341 0.0 0.0 0.62
GLY 39 A 1.0 0.3705 0.4117 0.6772 0.94 0.6365 0.0 0.0 0.5241
ALA 40 A 1.0 0.489 0.3846 0.8016 1.0 0.8016 0.0 0.0 0.6453
ARG 41 A 1.0 0.5109 0.5067 0.7641 1.0 0.7641 0.0 0.0 0.6375
VAL 42 A 0.8 0.6763 0.5656 0.7475 1.0 0.7475 0.0 0.0 0.7119
GLY 43 A 0.5 0.7337 0.4117 0.8915 1.0 0.8915 0.0 0.0 0.8126
TYR 44 A 0.5 0.7363 0.7963 0.7625 1.0 0.7625 0.0 0.0 0.7794
ILE 45 A 0.8 0.7024 0.638 0.557 0.98 0.5459 0.0 0.0 0.6702
GLU 46 A 1.0 0.6608 0.3348 0.6645 1.0 0.6645 0.0 0.0 0.6626
LEU 47 A 0.8 0.6131 0.7058 0.5707 1.0 0.5707 0.0 0.0 0.6594
ASP 48 A 1.0 0.4773 0.3212 0.6963 1.0 0.6963 0.0 0.0 0.5868
LEU 49 A 1.0 0.5763 0.7058 0.6209 1.0 0.6209 0.0 0.0 0.6634
ASN 50 A 1.0 0.3649 0.3936 0.4828 0.96 0.4635 0.0 0.0 0.4286
SER 51 A 1.0 0.3455 0.3574 0.4897 0.96 0.4702 0.0 0.0 0.4138
GLY 52 A 1.0 0.4463 0.4117 0.7399 0.98 0.7251 0.0 0.0 0.5857
LYS 53 A 1.0 0.3604 0.2488 0.3841 0.94 0.3611 0.0 0.0 0.3608
ILE 54 A 1.0 0.4851 0.638 0.3776 0.92 0.3473 0.0 0.0 0.5616
LEU 55 A 1.0 0.4936 0.7058 0.4812 0.98 0.4716 0.0 0.0 0.5997
GLU 56 A 1.0 0.558 0.3348 0.2356 0.54 0.1272 0.0 0.0 0.4464
SER 57 A 1.0 0.5527 0.3574 0.4512 0.86 0.388 0.0 0.0 0.4704
PHE 58 A 1.0 0.5465 1.0 0.4883 1.0 0.4883 0.0 0.0 0.7732
ARG 59 A 1.0 0.4849 0.5067 0.7882 1.0 0.7882 0.0 0.0 0.6475
PRO 60 A 1.0 0.5275 0.466 0.5851 0.98 0.5734 0.0 0.0 0.5504
GLU 61 A 1.0 0.4332 0.3348 0.5789 0.96 0.5557 0.0 0.0 0.4944
GLU 62 A 1.0 0.4866 0.3348 0.772 1.0 0.772 0.0 0.0 0.6293
ARG 63 A 1.0 0.5151 0.5067 0.7803 1.0 0.7803 0.0 0.0 0.6477
PHE 64 A 0.8 0.699 1.0 0.8392 1.0 0.8392 0.0 0.0 0.9196
PRO 65 A 0.8 0.7157 0.466 0.7796 1.0 0.7796 0.0 0.0 0.7476
MET 66 A 0.8 0.8332 0.6606 0.7335 1.0 0.7335 0.0 0.0 0.7834
MET 67 A 0.8 0.8131 0.6606 0.7926 1.0 0.7926 0.0 0.0 0.8029
SER 68 A 1.0 0.8463 0.3574 0.9572 1.0 0.9572 0.6355 1.0 0.9018
THR 69 A 0.5 0.9843 0.3257 0.8622 1.0 0.8622 0.0 0.0 0.9232
PHE 70 A 0.8 0.8894 1.0 0.7921 1.0 0.7921 0.0 0.0 0.9447
LYS 71 A 0.5 0.8959 0.2488 0.9589 1.0 0.9589 0.0 0.0 0.9274
VAL 72 A 0.5 0.9561 0.5656 0.6351 1.0 0.6351 0.0 0.0 0.7956
LEU 73 A 0.8 0.8761 0.7058 0.7186 1.0 0.7186 0.0 0.0 0.7974
LEU 74 A 0.5 0.858 0.7058 0.7184 1.0 0.7184 0.0 0.0 0.7882
CYS 75 A 0.5 0.8582 0.6425 0.7897 1.0 0.7897 0.0 0.0 0.824
GLY 76 A 0.5 0.7779 0.4117 0.6851 1.0 0.6851 0.0 0.0 0.7315
ALA 77 A 0.8 0.6935 0.3846 0.693 1.0 0.693 0.0 0.0 0.6932
VAL 78 A 0.5 0.7046 0.5656 0.6326 1.0 0.6326 0.0 0.0 0.6686
LEU 79 A 0.8 0.6453 0.7058 0.9168 1.0 0.9168 0.0 0.0 0.8113
SER 80 A 1.0 0.5395 0.3574 0.5117 0.98 0.5015 0.0 0.0 0.5205
ARG 81 A 1.0 0.4735 0.5067 0.6856 1.0 0.6856 0.0 0.0 0.5962
VAL 82 A 1.0 0.4813 0.5656 0.7089 1.0 0.7089 0.0 0.0 0.6372
ASP 83 A 1.0 0.4098 0.3212 0.8243 1.0 0.8243 0.0 0.0 0.617
ALA 84 A 1.0 0.3341 0.3846 0.371 1.0 0.371 0.0 0.0 0.3778
GLY 85 A 1.0 0.2913 0.4117 0.833 1.0 0.833 0.0 0.0 0.6224
GLN 86 A 1.0 0.3254 0.4343 0.3336 0.96 0.3202 0.0 0.0 0.3798
GLU 87 A 0.8 0.4682 0.3348 0.7056 1.0 0.7056 0.0 0.0 0.5869
GLN 88 A 1.0 0.3582 0.4343 0.4124 1.0 0.4124 0.0 0.0 0.4234
LEU 89 A 1.0 0.5127 0.7058 0.8865 1.0 0.8865 0.0 0.0 0.7961
GLY 90 A 1.0 0.3832 0.4117 0.5267 0.9 0.4741 0.0 0.0 0.4429
ARG 91 A 1.0 0.416 0.5067 0.6849 1.0 0.6849 0.0 0.0 0.5958
ARG 92 A 1.0 0.3542 0.5067 0.6188 1.0 0.6188 0.0 0.0 0.5628
ILE 93 A 1.0 0.5106 0.638 0.5855 0.98 0.5738 0.0 0.0 0.6059
HIS 94 A 1.0 0.3345 0.5972 0.3589 0.8 0.2871 0.0 0.0 0.4658
TYR 95 A 1.0 0.4788 0.7963 0.5885 1.0 0.5885 0.0 0.0 0.6924
SER 96 A 1.0 0.3264 0.3574 0.3839 1.0 0.3839 0.0 0.0 0.3707
GLN 97 A 1.0 0.2683 0.4343 0.3573 0.92 0.3287 0.0 0.0 0.3815
ASN 98 A 1.0 0.2567 0.3936 0.3483 0.94 0.3274 0.0 0.0 0.3605
ASP 99 A 1.0 0.4286 0.3212 0.7201 1.0 0.7201 0.0 0.0 0.5743
LEU 100 A 1.0 0.4296 0.7058 0.7247 1.0 0.7247 0.6192 1.0 0.7152
VAL 101 A 1.0 0.5086 0.5656 0.6393 1.0 0.6393 0.0 0.0 0.6024
GLU 102 A 1.0 0.4648 0.3348 0.413 0.86 0.3552 0.0 0.0 0.41
TYR 103 A 1.0 0.5424 0.7963 0.6543 1.0 0.6543 0.6695 1.0 0.7253
SER 104 A 1.0 0.5235 0.3574 0.7693 1.0 0.7693 0.564 1.0 0.6464
PRO 105 A 1.0 0.4902 0.466 0.8633 1.0 0.8633 0.6236 1.0 0.6768
VAL 106 A 1.0 0.5153 0.5656 0.6077 1.0 0.6077 0.0 0.0 0.5866
THR 107 A 0.5 0.5797 0.3257 0.7372 1.0 0.7372 0.0 0.0 0.6584
GLU 108 A 1.0 0.3832 0.3348 0.5514 1.0 0.5514 0.0 0.0 0.4673
LYS 109 A 1.0 0.33 0.2488 0.472 1.0 0.472 0.0 0.0 0.401
HIS 110 A 1.0 0.4044 0.5972 0.597 1.0 0.597 0.0 0.0 0.5971
LEU 111 A 1.0 0.3431 0.7058 0.5623 1.0 0.5623 0.0 0.0 0.634
THR 112 A 1.0 0.2267 0.3257 0.6024 1.0 0.6024 0.0 0.0 0.464
ASP 113 A 1.0 0.296 0.3212 0.4415 1.0 0.4415 0.0 0.0 0.3813
GLY 114 A 0.8 0.4171 0.4117 0.7344 1.0 0.7344 0.0 0.0 0.5758
MET 115 A 0.8 0.5403 0.6606 0.668 1.0 0.668 0.0 0.0 0.6643
THR 116 A 1.0 0.4768 0.3257 0.6601 1.0 0.6601 0.0 0.0 0.5684
VAL 117 A 0.5 0.6126 0.5656 0.5921 1.0 0.5921 0.0 0.0 0.6023
ARG 118 A 1.0 0.4881 0.5067 0.4469 1.0 0.4469 0.0 0.0 0.4974
GLU 119 A 1.0 0.5229 0.3348 0.6054 1.0 0.6054 0.0 0.0 0.5642
LEU 120 A 0.5 0.7037 0.7058 0.8074 1.0 0.8074 0.0 0.0 0.7566
CYS 121 A 0.5 0.7749 0.6425 0.8041 1.0 0.8041 0.0 0.0 0.7895
SER 122 A 1.0 0.6332 0.3574 0.5345 0.98 0.5238 0.0 0.0 0.5785
ALA 123 A 0.8 0.6798 0.3846 0.8645 1.0 0.8645 0.0 0.0 0.7722
ALA 124 A 0.5 0.8333 0.3846 0.7104 1.0 0.7104 0.0 0.0 0.7718
ILE 125 A 0.5 0.815 0.638 0.6368 1.0 0.6368 0.0 0.0 0.7265
THR 126 A 1.0 0.6349 0.3257 0.667 1.0 0.667 0.0 0.0 0.651
MET 127 A 1.0 0.5665 0.6606 0.5067 0.98 0.4966 0.0 0.0 0.6136
SER 128 A 1.0 0.7294 0.3574 0.9486 1.0 0.9486 0.6312 1.0 0.839
ASP 129 A 0.5 0.694 0.3212 0.9405 1.0 0.9405 0.0 0.0 0.8172
ASN 130 A 1.0 0.674 0.3936 0.8905 1.0 0.8905 0.6312 1.0 0.7822
THR 131 A 0.8 0.6281 0.3257 0.6701 1.0 0.6701 0.0 0.0 0.6491
ALA 132 A 0.5 0.7599 0.3846 0.902 1.0 0.902 0.0 0.0 0.831
ALA 133 A 0.5 0.8236 0.3846 0.7275 1.0 0.7275 0.0 0.0 0.7756
ASN 134 A 1.0 0.6487 0.3936 0.9255 1.0 0.9255 0.6217 1.0 0.7871
LEU 135 A 1.0 0.6292 0.7058 0.7598 1.0 0.7598 0.0 0.0 0.7328
LEU 136 A 0.5 0.7834 0.7058 0.8068 1.0 0.8068 0.0 0.0 0.7951
LEU 137 A 0.5 0.6911 0.7058 0.7842 1.0 0.7842 0.0 0.0 0.745
THR 138 A 1.0 0.505 0.3257 0.4486 0.88 0.3948 0.0 0.0 0.4499
THR 139 A 1.0 0.5607 0.3257 0.5776 0.92 0.5313 0.0 0.0 0.546
ILE 140 A 1.0 0.593 0.638 0.58 0.98 0.5684 0.0 0.0 0.6155
GLY 141 A 1.0 0.4358 0.4117 0.9101 1.0 0.9101 0.0 0.0 0.673
GLY 142 A 0.8 0.5189 0.4117 0.92 1.0 0.92 0.0 0.0 0.7194
PRO 143 A 1.0 0.5518 0.466 0.8312 1.0 0.8312 0.0 0.0 0.6915
LYS 144 A 1.0 0.354 0.2488 0.4453 0.94 0.4186 0.0 0.0 0.3863
GLU 145 A 1.0 0.4377 0.3348 0.5495 1.0 0.5495 0.0 0.0 0.4936
LEU 146 A 0.8 0.6906 0.7058 0.6933 1.0 0.6933 0.0 0.0 0.6996
THR 147 A 1.0 0.52 0.3257 0.788 1.0 0.788 0.0 0.0 0.654
ALA 148 A 1.0 0.4216 0.3846 0.5145 1.0 0.5145 0.0 0.0 0.468
PHE 149 A 1.0 0.5765 1.0 0.7179 1.0 0.7179 0.0 0.0 0.859
LEU 150 A 0.5 0.636 0.7058 0.6156 1.0 0.6156 0.0 0.0 0.6709
HIS 151 A 1.0 0.3909 0.5972 0.7796 1.0 0.7796 0.0 0.0 0.6884
ASN 152 A 1.0 0.3704 0.3936 0.4439 0.96 0.4262 0.0 0.0 0.4099
MET 153 A 1.0 0.522 0.6606 0.562 0.96 0.5395 0.0 0.0 0.6
GLY 154 A 1.0 0.4098 0.4117 0.901 1.0 0.901 0.0 0.0 0.6564
ASP 155 A 0.8 0.5428 0.3212 0.8998 1.0 0.8998 0.0 0.0 0.7213
HIS 156 A 1.0 0.3581 0.5972 0.3194 0.98 0.3131 0.0 0.0 0.4776
VAL 157 A 1.0 0.4988 0.5656 0.4669 0.98 0.4576 0.0 0.0 0.5322
THR 158 A 0.8 0.6713 0.3257 0.7055 1.0 0.7055 0.0 0.0 0.7055
ARG 159 A 1.0 0.5047 0.5067 0.8208 1.0 0.8208 0.0 0.0 0.8208
LEU 160 A 0.8 0.6849 0.7058 0.7638 1.0 0.7638 0.0 0.0 0.7638
ASP 161 A 1.0 0.5004 0.3212 0.8324 1.0 0.8324 0.0 0.0 0.8324
ARG 162 A 1.0 0.4994 0.5067 0.8001 1.0 0.8001 0.0 0.0 0.8001
TRP 163 A 1.0 0.5305 0.9909 0.4471 0.96 0.4292 0.6565 1.0 0.4292
GLU 164 A 0.8 0.675 0.3348 0.8706 1.0 0.8706 0.0 0.0 0.7728
PRO 165 A 1.0 0.5174 0.466 0.681 1.0 0.681 0.0 0.0 0.5992
GLU 166 A 1.0 0.4656 0.3348 0.472 0.9 0.4248 0.0 0.0 0.4452
LEU 167 A 0.8 0.6894 0.7058 0.8229 1.0 0.8229 0.0 0.0 0.7644
ASN 168 A 1.0 0.6465 0.3936 0.8211 1.0 0.8211 0.5738 1.0 0.7338
GLU 169 A 1.0 0.4575 0.3348 0.5883 1.0 0.5883 0.0 0.0 0.5229
ALA 170 A 1.0 0.5691 0.3846 0.674 1.0 0.674 0.0 0.0 0.6216
ILE 171 A 1.0 0.3772 0.638 0.3896 0.98 0.3818 0.0 0.0 0.5099
PRO 172 A 1.0 0.3669 0.466 0.7768 1.0 0.7768 0.0 0.0 0.6214
ASN 173 A 1.0 0.336 0.3936 0.6994 1.0 0.6994 0.0 0.0 0.5465
ASP 174 A 1.0 0.4217 0.3212 0.8039 1.0 0.8039 0.0 0.0 0.6128
GLU 175 A 1.0 0.4207 0.3348 0.579 0.96 0.5559 0.0 0.0 0.4883
ARG 176 A 1.0 0.423 0.5067 0.7876 1.0 0.7876 0.0 0.0 0.6472
ASP 177 A 0.8 0.6535 0.3212 0.918 1.0 0.918 0.0 0.0 0.7857
THR 178 A 1.0 0.6457 0.3257 0.8561 1.0 0.8561 0.0 0.0 0.7509
THR 179 A 0.5 0.7536 0.3257 0.8062 1.0 0.8062 0.0 0.0 0.7799
MET 180 A 1.0 0.5708 0.6606 0.7298 1.0 0.7298 0.0 0.0 0.6952
PRO 181 A 0.5 0.723 0.466 0.8848 1.0 0.8848 0.0 0.0 0.8039
ALA 182 A 1.0 0.598 0.3846 0.4338 0.96 0.4164 0.0 0.0 0.5072
ALA 183 A 1.0 0.6268 0.3846 0.809 1.0 0.809 0.0 0.0 0.7179
MET 184 A 0.5 0.8376 0.6606 0.7792 1.0 0.7792 0.0 0.0 0.8084
ALA 185 A 0.5 0.7466 0.3846 0.5576 1.0 0.5576 0.0 0.0 0.6521
THR 186 A 1.0 0.584 0.3257 0.4016 0.84 0.3373 0.0 0.0 0.4606
THR 187 A 0.8 0.7083 0.3257 0.735 1.0 0.735 0.0 0.0 0.7216
LEU 188 A 0.5 0.846 0.7058 0.8024 1.0 0.8024 0.0 0.0 0.8242
ARG 189 A 1.0 0.5527 0.5067 0.4245 0.96 0.4075 0.0 0.0 0.5297
LYS 190 A 1.0 0.5328 0.2488 0.392 1.0 0.392 0.0 0.0 0.4624
LEU 191 A 0.5 0.7328 0.7058 0.7264 1.0 0.7264 0.0 0.0 0.7296
LEU 192 A 0.8 0.7139 0.7058 0.629 1.0 0.629 0.0 0.0 0.7098
THR 193 A 1.0 0.5278 0.3257 0.5915 1.0 0.5915 0.0 0.0 0.5596
GLY 194 A 1.0 0.478 0.4117 0.8133 1.0 0.8133 0.0 0.0 0.6457
GLU 195 A 1.0 0.3446 0.3348 0.4892 0.9 0.4403 0.0 0.0 0.3924
LEU 196 A 1.0 0.5054 0.7058 0.4992 0.92 0.4593 0.0 0.0 0.6056
LEU 197 A 0.8 0.5703 0.7058 0.9434 1.0 0.9434 0.0 0.0 0.8246
THR 198 A 1.0 0.3877 0.3257 0.5824 1.0 0.5824 0.0 0.0 0.485
LEU 199 A 1.0 0.3445 0.7058 0.3969 0.8 0.3175 0.0 0.0 0.5252
ALA 200 A 1.0 0.386 0.3846 0.4251 0.98 0.4166 0.0 0.0 0.4013
SER 201 A 0.8 0.5245 0.3574 0.8076 1.0 0.8076 0.0 0.0 0.666
ARG 202 A 1.0 0.4966 0.5067 0.7406 1.0 0.7406 0.0 0.0 0.6236
GLN 203 A 1.0 0.4657 0.4343 0.3721 0.8 0.2977 0.0 0.0 0.45
GLN 204 A 1.0 0.5485 0.4343 0.5601 1.0 0.5601 0.0 0.0 0.5543
LEU 205 A 0.5 0.7577 0.7058 0.8828 1.0 0.8828 0.0 0.0 0.8202
ILE 206 A 1.0 0.6366 0.638 0.4625 0.92 0.4255 0.0 0.0 0.6373
ASP 207 A 1.0 0.5326 0.3212 0.4118 0.94 0.3871 0.0 0.0 0.4598
TRP 208 A 0.8 0.6672 0.9909 0.8299 1.0 0.8299 0.0 0.0 0.9104
MET 209 A 0.5 0.7957 0.6606 0.7864 1.0 0.7864 0.0 0.0 0.791
GLU 210 A 1.0 0.5437 0.3348 0.3948 1.0 0.3948 0.0 0.0 0.4692
ALA 211 A 1.0 0.5428 0.3846 0.5405 0.96 0.5189 0.0 0.0 0.5308
ASP 212 A 1.0 0.6481 0.3212 0.6863 1.0 0.6863 0.0 0.0 0.6672
LYS 213 A 1.0 0.474 0.2488 0.4409 0.96 0.4233 0.0 0.0 0.4486
VAL 214 A 1.0 0.6057 0.5656 0.8586 1.0 0.8586 0.6338 1.0 0.7322
ALA 215 A 0.5 0.6521 0.3846 0.848 1.0 0.848 0.0 0.0 0.75
GLY 216 A 1.0 0.5019 0.4117 0.556 1.0 0.556 0.0 0.0 0.529
PRO 217 A 1.0 0.4821 0.466 0.4396 1.0 0.4396 0.0 0.0 0.474
LEU 218 A 0.5 0.6631 0.7058 0.7855 1.0 0.7855 0.0 0.0 0.7456
LEU 219 A 0.8 0.7409 0.7058 0.7473 1.0 0.7473 0.0 0.0 0.7441
ARG 220 A 1.0 0.5678 0.5067 0.8248 1.0 0.8248 0.0 0.0 0.6963
SER 221 A 1.0 0.4591 0.3574 0.7973 1.0 0.7973 0.0 0.0 0.6282
ALA 222 A 1.0 0.4909 0.3846 0.7543 1.0 0.7543 0.0 0.0 0.6226
LEU 223 A 1.0 0.5015 0.7058 0.7806 0.98 0.765 0.0 0.0 0.7354
PRO 224 A 1.0 0.3538 0.466 0.8972 1.0 0.8972 0.0 0.0 0.6816
ALA 225 A 1.0 0.2464 0.3846 0.3912 0.88 0.3442 0.0 0.0 0.3644
GLY 226 A 1.0 0.2821 0.4117 0.5641 1.0 0.5641 0.0 0.0 0.4879
TRP 227 A 1.0 0.4327 0.9909 0.8583 1.0 0.8583 0.0 0.0 0.9246
PHE 228 A 1.0 0.5177 1.0 0.4604 0.96 0.442 0.0 0.0 0.7588
ILE 229 A 1.0 0.628 0.638 0.7273 1.0 0.7273 0.0 0.0 0.6826
ALA 230 A 0.5 0.7157 0.3846 0.7834 1.0 0.7834 0.0 0.0 0.7495
ASP 231 A 0.5 0.78 0.3212 0.8777 1.0 0.8777 0.0 0.0 0.8288
LYS 232 A 0.5 0.8575 0.2488 0.8946 1.0 0.8946 0.0 0.0 0.876
SER 233 A 0.8 0.793 0.3574 0.8829 1.0 0.8829 0.0 0.0 0.838
GLY 234 A 0.8 0.8195 0.4117 0.9476 1.0 0.9476 0.0 0.0 0.8836
ALA 235 A 1.0 0.6882 0.3846 0.6626 1.0 0.6626 0.0 0.0 0.6754
GLY 236 A 1.0 0.6274 0.4117 0.7509 1.0 0.7509 0.5643 1.0 0.6891
GLU 237 A 1.0 0.482 0.3348 0.4952 0.94 0.4654 0.0 0.0 0.4737
ARG 238 A 1.0 0.4196 0.5067 0.585 1.0 0.585 0.0 0.0 0.5458
GLY 239 A 1.0 0.5384 0.4117 0.7475 1.0 0.7475 0.0 0.0 0.643
SER 240 A 0.8 0.6602 0.3574 0.6542 1.0 0.6542 0.0 0.0 0.6572
ARG 241 A 1.0 0.7045 0.5067 0.5641 1.0 0.5641 0.0 0.0 0.6343
GLY 242 A 0.5 0.8695 0.4117 0.8193 1.0 0.8193 0.0 0.0 0.8444
ILE 243 A 0.5 0.8867 0.638 0.8821 1.0 0.8821 0.0 0.0 0.8844
ILE 244 A 0.5 1.0 0.638 0.6077 1.0 0.6077 0.0 0.0 0.819
ALA 245 A 0.5 0.8736 0.3846 0.832 1.0 0.832 0.0 0.0 0.8528
ALA 246 A 0.5 0.7637 0.3846 0.5933 1.0 0.5933 0.0 0.0 0.6785
LEU 247 A 0.8 0.6955 0.7058 0.522 0.98 0.5116 0.0 0.0 0.7006
GLY 248 A 0.5 0.5269 0.4117 0.7481 1.0 0.7481 0.0 0.0 0.6375
PRO 249 A 1.0 0.3818 0.466 0.8488 1.0 0.8488 0.0 0.0 0.6574
ASP 250 A 1.0 0.2685 0.3212 0.7141 0.98 0.6998 0.0 0.0 0.5105
GLY 251 A 1.0 0.3519 0.4117 0.7147 0.96 0.6861 0.0 0.0 0.5489
LYS 252 A 1.0 0.3777 0.2488 0.557 0.96 0.5347 0.0 0.0 0.4562
PRO 253 A 1.0 0.5517 0.466 0.4431 0.94 0.4165 0.0 0.0 0.5088
SER 254 A 1.0 0.5022 0.3574 0.7783 1.0 0.7783 0.0 0.0 0.6402
ARG 255 A 1.0 0.5697 0.5067 0.5295 1.0 0.5295 0.0 0.0 0.5496
ILE 256 A 0.5 0.7646 0.638 0.6104 1.0 0.6104 0.0 0.0 0.7013
VAL 257 A 0.5 0.8492 0.5656 0.5592 1.0 0.5592 0.0 0.0 0.7074
VAL 258 A 0.5 0.9025 0.5656 0.5984 1.0 0.5984 0.0 0.0 0.7505
ILE 259 A 0.5 0.8927 0.638 0.6416 1.0 0.6416 0.0 0.0 0.7672
TYR 260 A 0.8 0.8772 0.7963 0.7728 1.0 0.7728 0.0 0.0 0.8368
THR 261 A 0.8 0.7217 0.3257 0.6266 1.0 0.6266 0.0 0.0 0.6742
THR 262 A 1.0 0.6203 0.3257 0.595 1.0 0.595 0.0 0.0 0.6076
GLY 263 A 1.0 0.4815 0.4117 0.5253 0.94 0.4938 0.0 0.0 0.4876
SER 264 A 0.8 0.4788 0.3574 0.5525 0.98 0.5414 0.0 0.0 0.5101
GLN 265 A 1.0 0.3055 0.4343 0.3663 0.58 0.2124 0.0 0.0 0.3699
ALA 266 A 1.0 0.3944 0.3846 0.5192 1.0 0.5192 0.0 0.0 0.4568
THR 267 A 1.0 0.322 0.3257 0.4979 0.9 0.4481 0.0 0.0 0.3869
MET 268 A 1.0 0.4751 0.6606 0.5062 1.0 0.5062 0.5384 1.0 0.5834
ASP 269 A 1.0 0.3583 0.3212 0.401 0.96 0.3849 0.0 0.0 0.3716
GLU 270 A 1.0 0.3681 0.3348 0.4038 0.96 0.3876 0.0 0.0 0.3778
ARG 271 A 1.0 0.5589 0.5067 0.6372 1.0 0.6372 0.0 0.0 0.598
ASN 272 A 1.0 0.5374 0.3936 0.5862 1.0 0.5862 0.0 0.0 0.5618
ARG 273 A 1.0 0.3798 0.5067 0.5628 0.98 0.5516 0.0 0.0 0.5292
GLN 274 A 1.0 0.5361 0.4343 0.5753 0.98 0.5638 0.0 0.0 0.5499
ILE 275 A 0.5 0.7372 0.638 0.6805 1.0 0.6805 0.0 0.0 0.7088
ALA 276 A 1.0 0.5733 0.3846 0.7999 1.0 0.7999 0.0 0.0 0.6866
GLU 277 A 1.0 0.4906 0.3348 0.4883 0.84 0.4102 0.0 0.0 0.4504
ILE 278 A 0.8 0.7031 0.638 0.6801 1.0 0.6801 0.0 0.0 0.6916
GLY 279 A 0.5 0.6544 0.4117 0.6752 1.0 0.6752 0.0 0.0 0.6648
ALA 280 A 1.0 0.4945 0.3846 0.6462 1.0 0.6462 0.0 0.0 0.5704
SER 281 A 1.0 0.5238 0.3574 0.5353 0.9 0.4817 0.0 0.0 0.5028
LEU 282 A 0.8 0.6582 0.7058 0.5349 0.98 0.5242 0.0 0.0 0.682
ILE 283 A 1.0 0.508 0.638 0.4816 0.98 0.472 0.0 0.0 0.573
LYS 284 A 1.0 0.3538 0.2488 0.3331 0.68 0.2265 0.0 0.0 0.3013
HIS 285 A 1.0 0.4294 0.5972 0.1371 0.46 0.063 0.0 0.0 0.5133
TRP 286 A 1.0 0.4871 0.9909 0.2251 0.74 0.1666 0.0 0.0 0.739
AA pos chain pc tr freq trace
MET 1 A 0.6606 0.0 0.0 0.0
SER 2 A 0.3574 0.0 0.0 0.0
ILE 3 A 0.638 0.0 0.0 0.0
GLN 4 A 0.4343 0.1189 0.22 0.0261
HIS 5 A 0.5972 0.0763 0.18 0.0137
PHE 6 A 1.0 0.0465 0.04 0.0018
ARG 7 A 0.5067 0.0853 0.4 0.0341
VAL 8 A 0.5656 0.088 0.6 0.0528
ALA 9 A 0.3846 0.1063 0.56 0.0595
LEU 10 A 0.7058 0.0746 0.14 0.0104
ILE 11 A 0.638 0.0817 0.4 0.0327
PRO 12 A 0.466 0.09 0.4 0.036
PHE 13 A 1.0 0.1315 0.82 0.1078
PHE 14 A 1.0 0.0858 0.26 0.0223
ALA 15 A 0.3846 0.1997 0.84 0.1678
ALA 16 A 0.3846 0.2801 0.36 0.1008
PHE 17 A 1.0 0.1378 0.78 0.1074
CYS 18 A 0.6425 0.1642 0.6 0.0985
LEU 19 A 0.7058 0.2308 0.9 0.2077
PRO 20 A 0.466 0.2446 0.88 0.2152
VAL 21 A 0.5656 0.2416 0.62 0.1498
PHE 22 A 1.0 0.2421 0.46 0.1113
ALA 23 A 0.3846 0.3107 0.92 0.2858
HIS 24 A 0.5972 0.2717 0.66 0.1793
PRO 25 A 0.466 0.2763 0.86 0.2376
GLU 26 A 0.3348 0.298 0.82 0.2443
THR 27 A 0.3257 0.5272 0.98 0.5166
LEU 28 A 0.7058 0.3125 0.96 0.3
VAL 29 A 0.5656 0.2721 0.78 0.2122
LYS 30 A 0.2488 0.3511 0.88 0.309
VAL 31 A 0.5656 0.5904 1.0 0.5904
LYS 32 A 0.2488 0.4791 0.86 0.412
ASP 33 A 0.3212 0.4265 0.58 0.2473
ALA 34 A 0.3846 0.6508 1.0 0.6508
GLU 35 A 0.3348 0.826 1.0 0.826
ASP 36 A 0.3212 0.332 0.78 0.259
GLN 37 A 0.4343 0.4018 0.94 0.3777
LEU 38 A 0.7058 0.5015 1.0 0.5015
GLY 39 A 0.4117 0.6516 0.94 0.6125
ALA 40 A 0.3846 0.7891 1.0 0.7891
ARG 41 A 0.5067 0.7611 1.0 0.7611
VAL 42 A 0.5656 0.6983 1.0 0.6983
GLY 43 A 0.4117 0.9231 1.0 0.9231
TYR 44 A 0.7963 0.7409 1.0 0.7409
ILE 45 A 0.638 0.5836 0.98 0.5719
GLU 46 A 0.3348 0.6177 1.0 0.6177
LEU 47 A 0.7058 0.5381 1.0 0.5381
ASP 48 A 0.3212 0.7325 1.0 0.7325
LEU 49 A 0.7058 0.6244 1.0 0.6244
ASN 50 A 0.3936 0.4483 0.92 0.4124
SER 51 A 0.3574 0.4474 0.98 0.4385
GLY 52 A 0.4117 0.7082 1.0 0.7082
LYS 53 A 0.2488 0.3277 0.9 0.2949
ILE 54 A 0.638 0.4006 0.92 0.3686
LEU 55 A 0.7058 0.4637 0.98 0.4545
GLU 56 A 0.3348 0.3943 0.58 0.2287
SER 57 A 0.3574 0.3803 0.8 0.3042
PHE 58 A 1.0 0.4781 1.0 0.4781
ARG 59 A 0.5067 0.7779 1.0 0.7779
PRO 60 A 0.466 0.6132 0.98 0.6009
GLU 61 A 0.3348 0.5916 0.94 0.5561
GLU 62 A 0.3348 0.7667 1.0 0.7667
ARG 63 A 0.5067 0.7829 1.0 0.7829
PHE 64 A 1.0 0.8674 1.0 0.8674
PRO 65 A 0.466 0.7794 1.0 0.7794
MET 66 A 0.6606 0.683 1.0 0.683
MET 67 A 0.6606 0.7854 1.0 0.7854
SER 68 A 0.3574 0.9524 1.0 0.9524
THR 69 A 0.3257 0.862 1.0 0.862
PHE 70 A 1.0 0.7709 1.0 0.7709
LYS 71 A 0.2488 0.9509 1.0 0.9509
VAL 72 A 0.5656 0.6133 1.0 0.6133
LEU 73 A 0.7058 0.7036 0.98 0.6895
LEU 74 A 0.7058 0.7025 1.0 0.7025
CYS 75 A 0.6425 0.8082 1.0 0.8082
GLY 76 A 0.4117 0.6512 1.0 0.6512
ALA 77 A 0.3846 0.6874 1.0 0.6874
VAL 78 A 0.5656 0.5935 1.0 0.5935
LEU 79 A 0.7058 0.9274 1.0 0.9274
SER 80 A 0.3574 0.5041 0.98 0.494
ARG 81 A 0.5067 0.6744 1.0 0.6744
VAL 82 A 0.5656 0.6939 1.0 0.6939
ASP 83 A 0.3212 0.8106 1.0 0.8106
ALA 84 A 0.3846 0.42 0.96 0.4032
GLY 85 A 0.4117 0.8478 1.0 0.8478
GLN 86 A 0.4343 0.4545 0.94 0.4272
GLU 87 A 0.3348 0.6987 1.0 0.6987
GLN 88 A 0.4343 0.4268 0.96 0.4097
LEU 89 A 0.7058 0.8624 1.0 0.8624
GLY 90 A 0.4117 0.5253 0.92 0.4832
ARG 91 A 0.5067 0.6551 1.0 0.6551
ARG 92 A 0.5067 0.6002 1.0 0.6002
ILE 93 A 0.638 0.4976 0.98 0.4876
HIS 94 A 0.5972 0.4044 0.9 0.364
TYR 95 A 0.7963 0.5997 1.0 0.5997
SER 96 A 0.3574 0.3607 0.96 0.3463
GLN 97 A 0.4343 0.3743 0.98 0.3668
ASN 98 A 0.3936 0.3133 1.0 0.3133
ASP 99 A 0.3212 0.7001 1.0 0.7001
LEU 100 A 0.7058 0.7211 1.0 0.7211
VAL 101 A 0.5656 0.5999 1.0 0.5999
GLU 102 A 0.3348 0.4011 0.96 0.385
TYR 103 A 0.7963 0.64 1.0 0.64
SER 104 A 0.3574 0.7763 1.0 0.7763
PRO 105 A 0.466 0.8837 1.0 0.8837
VAL 106 A 0.5656 0.5636 1.0 0.5636
THR 107 A 0.3257 0.68 1.0 0.68
GLU 108 A 0.3348 0.542 0.98 0.5312
LYS 109 A 0.2488 0.3927 1.0 0.3927
HIS 110 A 0.5972 0.5881 1.0 0.5881
LEU 111 A 0.7058 0.5731 1.0 0.5731
THR 112 A 0.3257 0.5544 1.0 0.5544
ASP 113 A 0.3212 0.3606 0.96 0.3461
GLY 114 A 0.4117 0.7754 1.0 0.7754
MET 115 A 0.6606 0.6766 1.0 0.6766
THR 116 A 0.3257 0.6604 1.0 0.6604
VAL 117 A 0.5656 0.5974 1.0 0.5974
ARG 118 A 0.5067 0.4362 0.96 0.4187
GLU 119 A 0.3348 0.5595 1.0 0.5595
LEU 120 A 0.7058 0.8048 1.0 0.8048
CYS 121 A 0.6425 0.7594 1.0 0.7594
SER 122 A 0.3574 0.488 1.0 0.488
ALA 123 A 0.3846 0.8548 1.0 0.8548
ALA 124 A 0.3846 0.7273 1.0 0.7273
ILE 125 A 0.638 0.598 1.0 0.598
THR 126 A 0.3257 0.6685 1.0 0.6685
MET 127 A 0.6606 0.4617 0.98 0.4525
SER 128 A 0.3574 0.9481 1.0 0.9481
ASP 129 A 0.3212 0.9405 1.0 0.9405
ASN 130 A 0.3936 0.9095 1.0 0.9095
THR 131 A 0.3257 0.7027 1.0 0.7027
ALA 132 A 0.3846 0.8985 1.0 0.8985
ALA 133 A 0.3846 0.7168 1.0 0.7168
ASN 134 A 0.3936 0.9248 1.0 0.9248
LEU 135 A 0.7058 0.7404 1.0 0.7404
LEU 136 A 0.7058 0.83 1.0 0.83
LEU 137 A 0.7058 0.781 1.0 0.781
THR 138 A 0.3257 0.3711 0.94 0.3488
THR 139 A 0.3257 0.4939 0.96 0.4742
ILE 140 A 0.638 0.5588 1.0 0.5588
GLY 141 A 0.4117 0.9221 1.0 0.9221
GLY 142 A 0.4117 0.9171 1.0 0.9171
PRO 143 A 0.466 0.8397 1.0 0.8397
LYS 144 A 0.2488 0.3648 0.9 0.3283
GLU 145 A 0.3348 0.5476 1.0 0.5476
LEU 146 A 0.7058 0.7389 1.0 0.7389
THR 147 A 0.3257 0.7837 1.0 0.7837
ALA 148 A 0.3846 0.504 1.0 0.504
PHE 149 A 1.0 0.7287 1.0 0.7287
LEU 150 A 0.7058 0.6112 1.0 0.6112
HIS 151 A 0.5972 0.7747 1.0 0.7747
ASN 152 A 0.3936 0.425 0.96 0.408
MET 153 A 0.6606 0.4581 0.96 0.4398
GLY 154 A 0.4117 0.8623 1.0 0.8623
ASP 155 A 0.3212 0.8957 1.0 0.8957
HIS 156 A 0.5972 0.2818 0.96 0.2705
VAL 157 A 0.5656 0.4531 0.98 0.4441
THR 158 A 0.3257 0.7019 1.0 0.7019
ARG 159 A 0.5067 0.8091 1.0 0.8091
LEU 160 A 0.7058 0.7606 1.0 0.7606
ASP 161 A 0.3212 0.8179 1.0 0.8179
ARG 162 A 0.5067 0.8118 1.0 0.8118
TRP 163 A 0.9909 0.4217 0.96 0.4048
GLU 164 A 0.3348 0.8627 1.0 0.8627
PRO 165 A 0.466 0.6858 1.0 0.6858
GLU 166 A 0.3348 0.535 0.94 0.5029
LEU 167 A 0.7058 0.8346 1.0 0.8346
ASN 168 A 0.3936 0.8312 1.0 0.8312
GLU 169 A 0.3348 0.5699 1.0 0.5699
ALA 170 A 0.3846 0.6679 1.0 0.6679
ILE 171 A 0.638 0.3309 0.98 0.3243
PRO 172 A 0.466 0.775 1.0 0.775
ASN 173 A 0.3936 0.7097 1.0 0.7097
ASP 174 A 0.3212 0.8141 1.0 0.8141
GLU 175 A 0.3348 0.6269 0.96 0.6018
ARG 176 A 0.5067 0.793 1.0 0.793
ASP 177 A 0.3212 0.9192 1.0 0.9192
THR 178 A 0.3257 0.8578 1.0 0.8578
THR 179 A 0.3257 0.8116 1.0 0.8116
MET 180 A 0.6606 0.7428 1.0 0.7428
PRO 181 A 0.466 0.8968 1.0 0.8968
ALA 182 A 0.3846 0.3608 0.92 0.3319
ALA 183 A 0.3846 0.8123 1.0 0.8123
MET 184 A 0.6606 0.7583 1.0 0.7583
ALA 185 A 0.3846 0.5829 1.0 0.5829
THR 186 A 0.3257 0.3149 0.72 0.2267
THR 187 A 0.3257 0.6736 1.0 0.6736
LEU 188 A 0.7058 0.8609 1.0 0.8609
ARG 189 A 0.5067 0.4587 1.0 0.4587
LYS 190 A 0.2488 0.4026 0.98 0.3945
LEU 191 A 0.7058 0.7247 1.0 0.7247
LEU 192 A 0.7058 0.6253 1.0 0.6253
THR 193 A 0.3257 0.624 0.98 0.6115
GLY 194 A 0.4117 0.7908 1.0 0.7908
GLU 195 A 0.3348 0.4492 0.86 0.3863
LEU 196 A 0.7058 0.5504 0.96 0.5284
LEU 197 A 0.7058 0.9508 1.0 0.9508
THR 198 A 0.3257 0.6238 1.0 0.6238
LEU 199 A 0.7058 0.3805 0.9 0.3424
ALA 200 A 0.3846 0.3444 0.98 0.3375
SER 201 A 0.3574 0.8099 1.0 0.8099
ARG 202 A 0.5067 0.7575 1.0 0.7575
GLN 203 A 0.4343 0.3579 0.8 0.2863
GLN 204 A 0.4343 0.58 1.0 0.58
LEU 205 A 0.7058 0.8624 1.0 0.8624
ILE 206 A 0.638 0.3835 0.96 0.3681
ASP 207 A 0.3212 0.3549 0.92 0.3265
TRP 208 A 0.9909 0.8317 1.0 0.8317
MET 209 A 0.6606 0.7808 1.0 0.7808
GLU 210 A 0.3348 0.3629 0.98 0.3556
ALA 211 A 0.3846 0.4761 1.0 0.4761
ASP 212 A 0.3212 0.6903 1.0 0.6903
LYS 213 A 0.2488 0.4922 0.92 0.4528
VAL 214 A 0.5656 0.8561 1.0 0.8561
ALA 215 A 0.3846 0.8782 1.0 0.8782
GLY 216 A 0.4117 0.5439 1.0 0.5439
PRO 217 A 0.466 0.41 1.0 0.41
LEU 218 A 0.7058 0.7863 1.0 0.7863
LEU 219 A 0.7058 0.7428 1.0 0.7428
ARG 220 A 0.5067 0.8121 1.0 0.8121
SER 221 A 0.3574 0.7892 1.0 0.7892
ALA 222 A 0.3846 0.7214 1.0 0.7214
LEU 223 A 0.7058 0.7158 1.0 0.7158
PRO 224 A 0.466 0.885 1.0 0.885
ALA 225 A 0.3846 0.3701 0.78 0.2887
GLY 226 A 0.4117 0.605 1.0 0.605
TRP 227 A 0.9909 0.8609 1.0 0.8609
PHE 228 A 1.0 0.3733 1.0 0.3733
ILE 229 A 0.638 0.7067 1.0 0.7067
ALA 230 A 0.3846 0.779 1.0 0.779
ASP 231 A 0.3212 0.8807 1.0 0.8807
LYS 232 A 0.2488 0.888 1.0 0.888
SER 233 A 0.3574 0.8865 1.0 0.8865
GLY 234 A 0.4117 0.9445 1.0 0.9445
ALA 235 A 0.3846 0.6564 0.98 0.6433
GLY 236 A 0.4117 0.7357 0.98 0.7209
GLU 237 A 0.3348 0.5379 0.94 0.5056
ARG 238 A 0.5067 0.5564 1.0 0.5564
GLY 239 A 0.4117 0.7577 1.0 0.7577
SER 240 A 0.3574 0.6306 1.0 0.6306
ARG 241 A 0.5067 0.6065 1.0 0.6065
GLY 242 A 0.4117 0.8227 1.0 0.8227
ILE 243 A 0.638 0.8901 1.0 0.8901
ILE 244 A 0.638 0.6355 1.0 0.6355
ALA 245 A 0.3846 0.8326 1.0 0.8326
ALA 246 A 0.3846 0.5205 1.0 0.5205
LEU 247 A 0.7058 0.5266 1.0 0.5266
GLY 248 A 0.4117 0.7221 1.0 0.7221
PRO 249 A 0.466 0.846 1.0 0.846
ASP 250 A 0.3212 0.6597 1.0 0.6597
GLY 251 A 0.4117 0.7006 0.98 0.6866
LYS 252 A 0.2488 0.5441 0.98 0.5332
PRO 253 A 0.466 0.5196 0.82 0.4261
SER 254 A 0.3574 0.7731 1.0 0.7731
ARG 255 A 0.5067 0.5066 1.0 0.5066
ILE 256 A 0.638 0.6053 0.98 0.5932
VAL 257 A 0.5656 0.5454 1.0 0.5454
VAL 258 A 0.5656 0.5792 0.96 0.556
ILE 259 A 0.638 0.6305 1.0 0.6305
TYR 260 A 0.7963 0.7411 1.0 0.7411
THR 261 A 0.3257 0.6469 1.0 0.6469
THR 262 A 0.3257 0.6117 1.0 0.6117
GLY 263 A 0.4117 0.5274 0.96 0.5063
SER 264 A 0.3574 0.5703 0.98 0.5589
GLN 265 A 0.4343 0.3536 0.64 0.2263
ALA 266 A 0.3846 0.5041 1.0 0.5041
THR 267 A 0.3257 0.5037 0.92 0.4634
MET 268 A 0.6606 0.4767 1.0 0.4767
ASP 269 A 0.3212 0.4463 0.86 0.3838
GLU 270 A 0.3348 0.3459 1.0 0.3459
ARG 271 A 0.5067 0.6866 1.0 0.6866
ASN 272 A 0.3936 0.5813 1.0 0.5813
ARG 273 A 0.5067 0.541 1.0 0.541
GLN 274 A 0.4343 0.5579 0.98 0.5467
ILE 275 A 0.638 0.6625 1.0 0.6625
ALA 276 A 0.3846 0.7927 1.0 0.7927
GLU 277 A 0.3348 0.5175 0.72 0.3726
ILE 278 A 0.638 0.6661 1.0 0.6661
GLY 279 A 0.4117 0.6646 1.0 0.6646
ALA 280 A 0.3846 0.6007 0.96 0.5767
SER 281 A 0.3574 0.5172 0.96 0.4965
LEU 282 A 0.7058 0.5673 0.96 0.5446
ILE 283 A 0.638 0.5761 0.98 0.5646
LYS 284 A 0.2488 0.3268 0.48 0.1569
HIS 285 A 0.5972 0.166 0.44 0.073
TRP 286 A 0.9909 0.2312 0.66 0.1526
docs/_build/html/_sources/analysis.rst.txt
Analyzing and Modifying the PRESCOTT Output
Analyzing and Modifying the ESCOTT Output
==========================================
Raw PRESCOTT Scores and Their Interpretation
Raw ESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/_build/html/_sources/index.rst.txt
.. esgemme documentation master file, created by
.. PRESCOTT documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
Welcome to PRESCOTT documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction.rst
docker.rst
analysis.rst
input-preparation.rst
......
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<li class="toctree-l1"><a class="reference internal" href="introduction.html#prescott-population-aware-epistatic-and-structural-model-of-mutational-effects">PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html#cite">Cite</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
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<section id="analyzing-and-modifying-the-prescott-output">
<h1>Analyzing and Modifying the PRESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-prescott-output" title="Permalink to this heading"></a></h1>
<section id="raw-prescott-scores-and-their-interpretation">
<h2>Raw PRESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-prescott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw PRESCOTT scores. However, the values
<section id="analyzing-and-modifying-the-escott-output">
<h1>Analyzing and Modifying the ESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-escott-output" title="Permalink to this heading"></a></h1>
<section id="raw-escott-scores-and-their-interpretation">
<h2>Raw ESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-escott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.</p>
<p>We should note that most of the ‘impactful’ mutations are deleterious but
......@@ -91,7 +94,7 @@ it is not always the case.</p>
</section>
<section id="entire-single-point-mutation-landscape-calculations">
<h2>Entire Single Point Mutation Landscape Calculations<a class="headerlink" href="#entire-single-point-mutation-landscape-calculations" title="Permalink to this heading"></a></h2>
<p>By default, PRESCOTT will only output the combined (independent
<p>By default, ESCOTT will only output the combined (independent
and epistatic) scores*:</p>
<p>There are three output files:</p>
<ol class="arabic">
......@@ -143,7 +146,7 @@ D286F -0.23</p>
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<section id="welcome-to-prescott-documentation">
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......@@ -86,8 +95,8 @@
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<section id="introduction">
<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this heading"></a></h1>
<section id="what-is-prescott">
<h2>What is PRESCOTT?<a class="headerlink" href="#what-is-prescott" title="Permalink to this heading"></a></h2>
<p>PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
on population, evolutionary and structural information. It is made up of
two main programs: escott and prescott.</p>
<p>ESCOTT can calculate effects of single point mutations and multiple
point mutations. On the other hand, PRESCOTT incorporates population
frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
first to have predictions of mutational effects. We recommend using
PRESCOTT package via our web site or our docker image due to its
dependencies.</p>
</section>
<section id="input-data-requirements">
<h2>Input Data Requirements<a class="headerlink" href="#input-data-requirements" title="Permalink to this heading"></a></h2>
<section id="input-data-requirements-for-escott">
<h3>Input Data Requirements for escott<a class="headerlink" href="#input-data-requirements-for-escott" title="Permalink to this heading"></a></h3>
<p>escott requires two files:</p>
<ul class="simple">
<li><p>a multiple sequence alignment (MSA) file in fasta format (mandatory):</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Your</span> <span class="n">query</span> <span class="n">protein</span> <span class="n">must</span> <span class="n">be</span> <span class="n">the</span> <span class="n">first</span> <span class="n">sequence</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">fasta</span> <span class="n">file</span><span class="o">.</span> <span class="n">In</span> <span class="n">addition</span><span class="p">,</span> <span class="n">the</span> <span class="n">query</span> <span class="n">sequence</span> <span class="n">should</span> <span class="ow">not</span> <span class="n">contain</span> <span class="nb">any</span> <span class="n">gaps</span><span class="o">.</span>
</pre></div>
</div>
<ul class="simple">
<li><p>a structure file in PDB format (optional but highly recommended).</p></li>
</ul>
<p>One of the fastest ways to obtain both input MSA and a PDB file is to
run colabfold:
<a class="reference external" href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a></p>
<p>Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
such as ugene (<a class="reference external" href="http://ugene.net/">http://ugene.net/</a>) or jalview (<a class="reference external" href="https://www.jalview.org/">https://www.jalview.org/</a>).</p>
<p>For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.</p>
</section>
<section id="input-data-requirements-for-prescott">
<h3>Input Data Requirements for prescott<a class="headerlink" href="#input-data-requirements-for-prescott" title="Permalink to this heading"></a></h3>
<p>prescott requires three files:</p>
<ul class="simple">
<li><p>output file of escott (the file ending with …normPredCombi.txt)</p></li>
<li><p>a fasta file containing only your query sequence</p></li>
<li><p>gnomad csv file containing to be downloaded from <a class="reference external" href="https://gnomad.broadinstitute.org/">https://gnomad.broadinstitute.org/</a> for your protein.</p></li>
</ul>
</section>
</section>
<section id="usage">
<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading"></a></h2>
<p>You can find example bash scripts for escott and prescott in examples
folder of this repository.</p>
<p>Below, you will find examples of the most basic usage. Consult to the
documentation for further details.</p>
<section id="running-the-escott-program">
<h3>Running the escott program<a class="headerlink" href="#running-the-escott-program" title="Permalink to this heading"></a></h3>
<p>Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.</p>
<p>Run the program by issuing the following command in a bash terminal:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
</pre></div>
</div>
<p>A quick help can be accessed by typing</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott --help
</pre></div>
</div>
<p>By default, ESCOTT will predict the effect of all possible single
mutations at all positions in the query sequence. Alternatively, a set
of single or multiple mutations can be given with the option -m. Each
line of the file should contain a mutation (e.g. D136R) or combination
of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A).</p>
</section>
<section id="running-the-prescott-program">
<h3>Running the prescott program<a class="headerlink" href="#running-the-prescott-program" title="Permalink to this heading"></a></h3>
<p>A quick help can be accessed by typing</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prescott --help
</pre></div>
</div>
<p>Run the program by issuing the following command in a bash terminal:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
</pre></div>
</div>
<p>The most important output is prescott-scores.txt file, which produces
frequecy modified scores for the mutations.</p>
<p>Please note that the example input files for prescott are in the data
directory of this repository.</p>
</section>
</section>
<section id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h2>
<p>PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, you can find the
steps required to install it from the source in the following link (or
in the docs folder of this repository):</p>
</section>
<section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
<p>Coming soon…</p>
</section>
</section>
</div>
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<p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
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docs/_build/html/search.html
......@@ -44,8 +44,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......
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docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 27 SEP 2023 14:26
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 10 OCT 2023 10:32
entering extended mode
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......@@ -775,68 +775,74 @@ File: umsb.fd 2013/01/14 v3.01 AMS symbols B
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 4.
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[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for PRESCOTT: I. An in-put MSA:
[]
[8]
Chapter 4.
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Chapter 5.
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[]\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc
. fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the
[]
[11] [12
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Chapter 5.
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Chapter 6.
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docs/_build/latex/prescott.tex
......@@ -61,7 +61,7 @@
\title{prescott}
\date{Sep 27, 2023}
\date{Oct 10, 2023}
\release{1.5.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -85,6 +85,168 @@
\sphinxstepscope
\chapter{Introduction}
\label{\detokenize{introduction:introduction}}\label{\detokenize{introduction::doc}}
\section{What is PRESCOTT?}
\label{\detokenize{introduction:what-is-prescott}}
\sphinxAtStartPar
PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
on population, evolutionary and structural information. It is made up of
two main programs: escott and prescott.
\sphinxAtStartPar
ESCOTT can calculate effects of single point mutations and multiple
point mutations. On the other hand, PRESCOTT incorporates population
frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
first to have predictions of mutational effects. We recommend using
PRESCOTT package via our web site or our docker image due to its
dependencies.
\section{Input Data Requirements}
\label{\detokenize{introduction:input-data-requirements}}
\subsection{Input Data Requirements for escott}
\label{\detokenize{introduction:input-data-requirements-for-escott}}
\sphinxAtStartPar
escott requires two files:
\begin{itemize}
\item {}
\sphinxAtStartPar
a multiple sequence alignment (MSA) file in fasta format (mandatory):
\end{itemize}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n}{Your} \PYG{n}{query} \PYG{n}{protein} \PYG{n}{must} \PYG{n}{be} \PYG{n}{the} \PYG{n}{first} \PYG{n}{sequence} \PYG{o+ow}{in} \PYG{n}{the} \PYG{n}{fasta} \PYG{n}{file}\PYG{o}{.} \PYG{n}{In} \PYG{n}{addition}\PYG{p}{,} \PYG{n}{the} \PYG{n}{query} \PYG{n}{sequence} \PYG{n}{should} \PYG{o+ow}{not} \PYG{n}{contain} \PYG{n+nb}{any} \PYG{n}{gaps}\PYG{o}{.}
\end{sphinxVerbatim}
\begin{itemize}
\item {}
\sphinxAtStartPar
a structure file in PDB format (optional but highly recommended).
\end{itemize}
\sphinxAtStartPar
One of the fastest ways to obtain both input MSA and a PDB file is to
run colabfold:
\sphinxurl{https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb}
\sphinxAtStartPar
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
\sphinxAtStartPar
For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.
\subsection{Input Data Requirements for prescott}
\label{\detokenize{introduction:input-data-requirements-for-prescott}}
\sphinxAtStartPar
prescott requires three files:
\begin{itemize}
\item {}
\sphinxAtStartPar
output file of escott (the file ending with …normPredCombi.txt)
\item {}
\sphinxAtStartPar
a fasta file containing only your query sequence
\item {}
\sphinxAtStartPar
gnomad csv file containing to be downloaded from \sphinxurl{https://gnomad.broadinstitute.org/} for your protein.
\end{itemize}
\section{Usage}
\label{\detokenize{introduction:usage}}
\sphinxAtStartPar
You can find example bash scripts for escott and prescott in examples
folder of this repository.
\sphinxAtStartPar
Below, you will find examples of the most basic usage. Consult to the
documentation for further details.
\subsection{Running the escott program}
\label{\detokenize{introduction:running-the-escott-program}}
\sphinxAtStartPar
Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.
\sphinxAtStartPar
Run the program by issuing the following command in a bash terminal:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott inputAli.fasta \PYGZhy{}f inputAli.fasta \PYGZhy{}\PYGZhy{}pdbfile input.pdb
\end{sphinxVerbatim}
\sphinxAtStartPar
A quick help can be accessed by typing
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott \PYGZhy{}\PYGZhy{}help
\end{sphinxVerbatim}
\sphinxAtStartPar
By default, ESCOTT will predict the effect of all possible single
mutations at all positions in the query sequence. Alternatively, a set
of single or multiple mutations can be given with the option \sphinxhyphen{}m. Each
line of the file should contain a mutation (e.g. D136R) or combination
of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A).
\subsection{Running the prescott program}
\label{\detokenize{introduction:running-the-prescott-program}}
\sphinxAtStartPar
A quick help can be accessed by typing
\begin{sphinxVerbatim}[commandchars=\\\{\}]
prescott \PYGZhy{}\PYGZhy{}help
\end{sphinxVerbatim}
\sphinxAtStartPar
Run the program by issuing the following command in a bash terminal:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
prescott \PYGZhy{}e ../data/MLH1\PYGZus{}normPred\PYGZus{}evolCombi.txt \PYGZhy{}g ../data/gnomAD\PYGZus{}v2.1.1\PYGZus{}MLH1\PYGZus{}HUMAN\PYGZus{}ENSG00000076242.csv \PYGZhy{}s ../data/MLH1.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
The most important output is prescott\sphinxhyphen{}scores.txt file, which produces
frequecy modified scores for the mutations.
\sphinxAtStartPar
Please note that the example input files for prescott are in the data
directory of this repository.
\section{Installation}
\label{\detokenize{introduction:installation}}
\sphinxAtStartPar
PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, you can find the
steps required to install it from the source in the following link (or
in the docs folder of this repository):
\section{Citation}
\label{\detokenize{introduction:citation}}
\sphinxAtStartPar
Coming soon…
\sphinxstepscope
\chapter{Using ESCOTT via Docker}
\label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}}
......@@ -258,13 +420,13 @@ mutation and its predicted effect, separated by a space.
\sphinxstepscope
\chapter{Analyzing and Modifying the PRESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-prescott-output}}\label{\detokenize{analysis::doc}}
\chapter{Analyzing and Modifying the ESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-escott-output}}\label{\detokenize{analysis::doc}}
\section{Raw PRESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-prescott-scores-and-their-interpretation}}
\section{Raw ESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-escott-scores-and-their-interpretation}}
\sphinxAtStartPar
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between {[}\sphinxhyphen{}12, 2{]} generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -276,7 +438,7 @@ it is not always the case.
\section{Entire Single Point Mutation Landscape Calculations}
\label{\detokenize{analysis:entire-single-point-mutation-landscape-calculations}}
\sphinxAtStartPar
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
\sphinxAtStartPar
......
docs/_build/latex/prescott.toc
\babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Using ESCOTT via Docker}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}Requirements}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}%
\contentsline {section}{\numberline {1.3}Single point mutation calculations}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Obtaining the entire single point mutation landscape}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Predicting the effect of a subset of single point mutations}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Multiple point mutation calculations}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Analyzing and Modifying the PRESCOTT Output}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Raw PRESCOTT Scores and Their Interpretation}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}%
\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}%
\contentsline {section}{\numberline {3.1}Preparing Your Input MSA and PDB with Colabfold}{7}{section.3.1}%
\contentsline {chapter}{\numberline {4}Installation}{9}{chapter.4}%
\contentsline {section}{\numberline {4.1}Installing the dependencies:}{9}{section.4.1}%
\contentsline {section}{\numberline {4.2}Preparation of the environment and installation of PRESCOTT}{9}{section.4.2}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{11}{section.4.3}%
\contentsline {chapter}{\numberline {5}Indices and tables}{13}{chapter.5}%
\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
\contentsline {chapter}{\numberline {3}Analyzing and Modifying the ESCOTT Output}{9}{chapter.3}%
\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}%
\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}%
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
\contentsline {chapter}{\numberline {5}Installation}{13}{chapter.5}%
\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}%
\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}%
\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}%
\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}%
docs/analysis.rst
Analyzing and Modifying the PRESCOTT Output
Analyzing and Modifying the ESCOTT Output
==========================================
Raw PRESCOTT Scores and Their Interpretation
Raw ESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/index.rst
.. esgemme documentation master file, created by
.. PRESCOTT documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
Welcome to PRESCOTT documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction.rst
docker.rst
analysis.rst
input-preparation.rst
......
docs/introduction.rst 0 → 100644
Introduction
============
What is PRESCOTT?
-----------------
PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
on population, evolutionary and structural information. It is made up of
two main programs: escott and prescott.
ESCOTT can calculate effects of single point mutations and multiple
point mutations. On the other hand, PRESCOTT incorporates population
frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
first to have predictions of mutational effects. We recommend using
PRESCOTT package via our web site or our docker image due to its
dependencies.
Input Data Requirements
-----------------------
Input Data Requirements for escott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
escott requires two files:
* a multiple sequence alignment (MSA) file in fasta format (mandatory):
::
Your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.
* a structure file in PDB format (optional but highly recommended).
One of the fastest ways to obtain both input MSA and a PDB file is to
run colabfold:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.
Input Data Requirements for prescott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prescott requires three files:
* output file of escott (the file ending with …normPredCombi.txt)
* a fasta file containing only your query sequence
* gnomad csv file containing to be downloaded from https://gnomad.broadinstitute.org/ for your protein.
Usage
-----
You can find example bash scripts for escott and prescott in examples
folder of this repository.
Below, you will find examples of the most basic usage. Consult to the
documentation for further details.
Running the escott program
~~~~~~~~~~~~~~~~~~~~~~~~~~
Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.
Run the program by issuing the following command in a bash terminal:
.. code:: bash
escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
A quick help can be accessed by typing
.. code:: bash
escott --help
By default, ESCOTT will predict the effect of all possible single
mutations at all positions in the query sequence. Alternatively, a set
of single or multiple mutations can be given with the option -m. Each
line of the file should contain a mutation (e.g. D136R) or combination
of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A).
Running the prescott program
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A quick help can be accessed by typing
.. code:: bash
prescott --help
Run the program by issuing the following command in a bash terminal:
.. code:: bash
prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
The most important output is prescott-scores.txt file, which produces
frequecy modified scores for the mutations.
Please note that the example input files for prescott are in the data
directory of this repository.
Installation
------------
PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, you can find the
steps required to install it from the source in the following link (or
in the docs folder of this repository):
Citation
--------
Coming soon…
.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
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