close all clear all UORF_init; %% Reference LamSh=[0:0.005:0.2]'; Lam=[0:0.005:0.1]'; denv3_50_100_50_08_0_03_03=[0 277 444 461 436 427 410 358 343 304 261 222 236 208 165 170 126 147 141 106 132 135 132 104 103 91 114 117 106 132 126 114 122 101 105 94 106 116 101 109 124 ]'; denv3_t50_100_50_08_0_03_03=[0 244 404 414 471 459 391 339 343 291 280 268 202 216 170 167 158 142 99 126 115 137 129 124 119 115 119 117 109 102 102 108 119 110 101 112 120 92 92 117 112 ]'; % End Reference %% Length variation v3_50_200_50_08_0_03_03_10_10_0=[0 220 339 356 345 299 297 202 172 149 126 82 61 72 58 51 53 41 28 30 27 23 34 34 24 28 12 30 16 21 25 22 26 30 23 25 17 27 17 16 23 ]'; v3_50_50_50_08_0_03_03_10_10_0=[0 267 457 562 557 613 589 532 517 497 444 434 382 426 389 379 418 383 354 351 334 347 303 339 313 349 319 326 313 326 297 372 331 324 298 310 333 293 287 290 318 ]'; v3_50_20_50_08_0_03_03_10_10_0=[0 243 450 582 723 733 744 759 803 815 782 802 777 799 809 828 786 802 790 766 779 795 776 781 798 785 780 799 784 767 818 743 774 770 784 761 773 713 742 769 787 ]'; v3_50_10_50_08_0_03_03_10_10_0=[0 288 519 608 746 837 889 944 970 920 1028 1035 1102 1052 1076 1088 1070 1010 1102 1134 1052 1080 1055 1132 1052 1061 1079 1143 1128 1128 1055 1039 1109 1053 1120 1024 1041 1152 1094 1063 1086 ]'; v3_50_2_50_08_0_03_03_10_10_0=[0 290 484 682 824 979 955 1069 1073 1124 1172 1160 1204 1252 1239 1315 1251 1272 1338 1406 1344 1304 1307 1371 1360 1305 1316 1379 1300 1370 1260 1364 1341 1338 1369 1324 1329 1371 1339 1332 1343 ]'; v3_50_40_50_08_0_03_03_10_10_0=[0 292 429 547 576 617 653 631 588 560 524 545 515 476 476 519 486 474 408 458 451 436 418 453 412 459 449 425 439 416 435 437 427 411 419 417 409 418 419 464 406 ]'; v3_50_30_50_08_0_03_03_10_10_0=[0 273 407 561 670 709 651 677 689 655 671 609 638 628 628 637 619 589 588 555 646 578 609 590 530 550 550 567 570 546 584 568 600 553 623 562 517 541 544 542 567 ]'; % No uORF v3_den50_100_50_0_0_03_03_10_10_0=[0 4271 7473 9900 11867 13500 14449 15583 16266 16975 17427 17690 17964 18246 18409 18507 18554 18628 18681 18700 18697 18730 18740 18766 18769 18792 18807 18784 18786 18828 18791 18792 18803 18811 18784 18796 18794 18792 18790 18798 18811 ]'; %Ribosome lengths variations %05.13.2018 We know the length of elongating ribosome. only scanning has to %be varied. v3_50_100_50_08_0_03_03_10_6_0=[0 250 411 412 396 250 173 76 28 19 15 15 9 8 14 14 11 10 6 6 11 ]'; v3_50_100_50_08_0_03_03_10_8_0=[0 262 395 403 423 357 319 243 198 142 76 72 47 46 36 35 39 44 36 44 27 36 23 33 29 18 26 32 30 28 26 32 33 31 23 38 39 39 22 31 31 ]'; v3_50_100_50_08_0_03_03_10_9_0=[0 268 381 440 445 416 377 316 251 230 154 158 122 115 97 79 78 76 74 68 71 ]'; v3_50_100_50_08_0_03_03_10_11_0=[0 245 389 447 492 457 468 420 359 343 350 289 267 246 279 275 237 246 229 220 229 ]'; v3_50_100_50_08_0_03_03_10_12_0=[0 250 348 454 473 519 497 432 438 421 422 392 374 356 334 328 288 293 337 311 338 289 274 277 292 302 314 285 297 264 282 267 279 294 274 291 266 269 279 274 272 ]'; v3_50_100_50_08_0_03_03_10_14_0=[0 273 415 483 507 502 497 507 480 519 437 441 461 479 460 456 441 453 451 386 420 ]'; % ELongating speed den50_100_50_08_0_03_03=[0 245 397 447 441 411 400 358 312 270 251 216 229 199 174 168 142 139 126 138 141]'; den50_100_50_08_0_03_02=[0 270 342 287 163 84 25 16 14 12 11 13 6 8 18 17 16 17 10 7 14 ]'; den50_100_50_08_0_03_024=[0 255 411 432 367 276 184 108 75 53 51 34 34 37 30 16 20 27 30 29 35 ]'; den50_100_50_08_0_03_028=[0 278 440 476 481 386 376 358 262 251 203 144 111 114 104 112 94 94 84 81 66 ]'; den50_100_50_08_0_03_032=[0 273 386 428 399 387 394 361 320 330 235 248 268 230 228 197 201 168 165 188 192 ]'; den50_100_50_08_0_03_035=[0 219 330 332 335 350 313 267 245 245 217 210 217 190 166 178 162 166 174 132 156 ]'; % Initiation rate den50_100_50_03_0_03_03=[0 1571 2560 3173 3350 3550 3474 3619 3605 3394 3361 3336 3270 3181 3292 3037 3082 3009 2961 2999 2858 ]'; den50_100_50_05_0_03_03=[0 950 1394 1576 1764 1688 1721 1591 1466 1469 1323 1284 1265 1149 1114 1045 1187 1018 1007 1030 943 ]'; den50_100_50_07_0_03_03=[0 402 663 785 768 726 684 673 581 546 468 522 414 410 408 334 324 302 250 293 294 ]'; den50_100_50_09_0_03_03=[0 117 194 220 202 199 173 146 122 125 104 80 91 51 68 55 63 50 46 45 45 ]'; % ReInitiation rate den50_100_50_08_0055_03_03=[0 453 737 903 967 1034 1042 973 1000 1001 964 945 866 897 915 893 872 839 869 876 843 ]'; den50_100_50_08_004_03_03=[0 390 683 776 833 859 843 892 834 779 752 771 793 725 744 674 654 683 679 643 661 ]'; den50_100_50_08_0025_03_03=[0 359 570 646 675 725 691 687 639 657 559 578 574 519 512 484 503 479 465 489 493 ]'; den50_100_50_08_001_03_03=[0 279 445 513 555 550 499 484 441 409 411 353 348 327 283 289 290 289 264 264 241 ]'; %Scannnig Death variation v3_50_100_50_08_0_03_03_10_10_s00001=[0 220 413 504 450 437 432 344 331 280 256 241 204 170 161 143 149 152 140 123 119 ]'; v3_50_100_50_08_0_03_03_10_10_s00002=[0 234 361 415 439 432 371 374 343 313 249 234 218 191 173 170 166 139 137 159 130 ]'; v3_50_100_50_08_0_03_03_10_10_s00005=[0 235 348 391 424 432 413 356 327 296 260 267 198 218 185 172 185 168 137 143 140 ]'; v3_50_100_50_08_0_03_03_10_10_s0001=[0 201 354 369 383 376 368 334 347 292 252 249 236 217 195 179 161 176 143 170 166 ]'; v3_50_100_50_08_0_03_03_10_10_s0002=[0 191 285 305 367 339 320 316 284 273 236 248 210 234 199 176 190 193 157 182 168 ]'; v3_50_100_50_08_0_03_03_10_10_s0005=[0 106 150 192 210 212 216 210 202 210 203 221 201 184 170 188 164 176 157 152 159 ]'; v3_50_100_50_08_0_03_03_10_10_s0003=[0 177 209 271 312 274 292 258 254 224 205 210 218 224 195 178 166 192 186 180 165 ]'; v3_50_100_50_08_0_03_03_10_10_0007_0=[0 73 129 134 143 165 168 149 147 145 147 142 167 150 141 145 167 131 134 131 138 ]'; %Elongating Death variation v3_50_100_50_08_0_03_03_10_10_e00001=[0 321 389 414 468 442 423 388 342 340 274 222 228 170 187 159 145 144 165 116 140 ]'; v3_50_100_50_08_0_03_03_10_10_e00002=[0 255 402 439 481 441 438 384 321 305 265 254 213 222 180 187 147 156 133 155 143 ]''; v3_50_100_50_08_0_03_03_10_10_e00004=[0 268 422 427 455 429 431 401 367 313 275 271 242 201 206 184 166 165 150 148 154 ]'; v3_50_100_50_08_0_03_03_10_10_e00006=[0 278 374 438 448 391 439 368 334 309 291 224 255 233 174 161 201 157 175 160 168 ]'; v3_50_100_50_08_0_03_03_10_10_e0001=[0 262 376 473 465 452 465 366 357 356 299 287 266 253 238 190 177 210 204 169 199 ]'; v3_50_100_50_08_0_03_03_10_10_e0005=[0 262 394 488 518 555 551 541 439 419 457 389 354 368 365 353 365 341 362 360 343 ]'; v3_50_100_50_08_0_03_03_10_10_e0003=[0 279 417 475 509 499 450 483 432 399 376 377 345 300 276 269 287 279 277 292 263 ]'; v3_50_100_50_08_0_03_03_10_10_e0007=[0 260 406 499 576 561 565 528 536 507 525 440 408 437 475 438 379 406 414 384 411 ]'; % survival variation survv3_50_100_50_08_0_03_03_10_10_0=[0 304 466 690 841 929 1003 1123 1162 1143 1205 1292 1303 1240 1269 1236 1351 1310 1335 1348 1292 ]'; survv3_50_100_50_08_0_03_03_10_10_0001=[0 215 441 553 712 759 824 955 876 996 991 1056 1020 1047 1042 1070 1078 1114 1091 1132 1106 ]'; survv3_50_100_50_08_0_03_03_10_10_001=[0 43 93 100 125 144 113 145 150 184 161 176 203 192 177 193 208 197 170 206 198 ]'; %delay variation den_del_05_50_100_50_08_0_03_03=[0 266 408 461 446 444 418 362 313 303 283 220 186 203 165 156 135 134 136 130 133 127 136 127 127 139 124 100 132 122 105 133 126 110 116 112 125 120 117 121 107 ]'; den_del_02_50_100_50_08_0_03_03=[0 250 409 461 441 444 410 387 366 270 278 205 220 210 216 198 154 162 150 154 151 153 161 132 157 142 143 141 149 143 155 146 130 146 154 147 148 120 147 168 142 ]'; den_del_01_50_100_50_08_0_03_03=[0 248 411 498 506 446 420 383 321 321 286 257 246 249 217 220 200 228 246 224 215 202 177 215 247 221 203 225 214 189 202 219 236 227 203 220 199 190 236 219 217 ]'; den_del_005_50_100_50_08_0_03_03=[0 255 401 444 513 445 427 378 378 309 380 341 335 313 332 350 334 297 299 320 329 321 360 307 347 355 327 344 325 314 307 310 326 320 299 346 325 317 309 270 313 ]'; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Saving for Grace %Ribosome Length variation dataElongatingLength=[Lam,v3_50_100_50_08_0_03_03_10_6_0./(TTime/10^3),v3_50_100_50_08_0_03_03_10_8_0(1:21)./(TTime/10^3),v3_50_100_50_08_0_03_03_10_9_0./(TTime/10^3),den50_100_50_08_0_03_03./(TTime/10^3),v3_50_100_50_08_0_03_03_10_11_0./(TTime/10^3),v3_50_100_50_08_0_03_03_10_12_0(1:21)./(TTime/10^3),v3_50_100_50_08_0_03_03_10_14_0./(TTime/10^3)]; save('ElogatingLength_abs.dat', 'dataElongatingLength','-ascii'); dataElongatingLength=[Lam,dataAver(v3_50_100_50_08_0_03_03_10_6_0),dataAver(v3_50_100_50_08_0_03_03_10_8_0(1:21)),dataAver(v3_50_100_50_08_0_03_03_10_9_0),dataAver(den50_100_50_08_0_03_03),dataAver(v3_50_100_50_08_0_03_03_10_11_0),dataAver(v3_50_100_50_08_0_03_03_10_12_0(1:21)),dataAver(v3_50_100_50_08_0_03_03_10_14_0)]; save('ElogatingLength_rel.dat', 'dataElongatingLength','-ascii'); %uORF Length variation ttt=[LamSh,dataAver(denv3_50_100_50_08_0_03_03),dataAver(v3_50_200_50_08_0_03_03_10_10_0),dataAver(v3_50_50_50_08_0_03_03_10_10_0),dataAver(v3_50_40_50_08_0_03_03_10_10_0),dataAver(v3_50_30_50_08_0_03_03_10_10_0),dataAver(v3_50_20_50_08_0_03_03_10_10_0),dataAver(v3_50_10_50_08_0_03_03_10_10_0),dataAver(v3_50_2_50_08_0_03_03_10_10_0),dataAver(v3_den50_100_50_0_0_03_03_10_10_0)]; %save('nouorf_rel.dat', 'ttt','-ascii'); ttt=[LamSh,denv3_50_100_50_08_0_03_03./(TTime/10^3),v3_50_200_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_50_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_40_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_30_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_20_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_10_50_08_0_03_03_10_10_0./(TTime/10^3),v3_50_2_50_08_0_03_03_10_10_0./(TTime/10^3),v3_den50_100_50_0_0_03_03_10_10_0./(5*TTime/10^3)]; %save('nouorf_abs.dat', 'ttt','-ascii'); %Elongating speed variation ttt=[Lam,den50_100_50_08_0_03_03./(TTime/10^3),den50_100_50_08_0_03_02./(TTime/10^3),den50_100_50_08_0_03_024./(TTime/10^3),den50_100_50_08_0_03_028./(TTime/10^3),den50_100_50_08_0_03_032./(TTime/10^3),den50_100_50_08_0_03_035./(TTime/10^3)]; %save('elongating_speed_abs.dat', 'ttt','-ascii'); ttt=[Lam,dataAver(den50_100_50_08_0_03_03),dataAver(den50_100_50_08_0_03_02),dataAver(den50_100_50_08_0_03_024),dataAver(den50_100_50_08_0_03_028),dataAver(den50_100_50_08_0_03_032),dataAver(den50_100_50_08_0_03_035)]; %save('elongating_speed_rel.dat', 'ttt','-ascii'); %initiation variation ttt=[Lam,den50_100_50_08_0_03_03./(TTime/10^3),den50_100_50_09_0_03_03./(TTime/10^3),den50_100_50_07_0_03_03./(TTime/10^3),den50_100_50_05_0_03_03./(TTime/10^3),den50_100_50_03_0_03_03./(TTime/10^3)]; %save('initiation_abs.dat', 'ttt','-ascii'); ttt=[Lam,dataAver(den50_100_50_08_0_03_03),dataAver(den50_100_50_09_0_03_03),dataAver(den50_100_50_07_0_03_03),dataAver(den50_100_50_05_0_03_03),dataAver(den50_100_50_03_0_03_03)]; %save('initiation_rel.dat', 'ttt','-ascii'); %reinitiation variation ttt=[Lam,den50_100_50_08_0_03_03./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_s0001./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_s0003./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_s0005./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_0007_0./(TTime/10^3)]; save('dissolution_scanning_abs.dat', 'ttt','-ascii'); ttt=[Lam,den50_100_50_08_0_03_03./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_e0001./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_e0003./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_e0005./(TTime/10^3),v3_50_100_50_08_0_03_03_10_10_e0007./(TTime/10^3)]; save('dissolution_elongating_abs.dat', 'ttt','-ascii'); ttt=[Lam,survv3_50_100_50_08_0_03_03_10_10_0./(TTime/10^3),survv3_50_100_50_08_0_03_03_10_10_0001./(TTime/10^3),survv3_50_100_50_08_0_03_03_10_10_001./(TTime/10^3)]; %save('Scanning_survive_abs.dat', 'ttt','-ascii'); ttt=[Lam,den50_100_50_08_0_03_03./(TTime/10^3),den_del_02_50_100_50_08_0_03_03(1:21)./(TTime/10^3),den_del_01_50_100_50_08_0_03_03(1:21)./(TTime/10^3),den_del_005_50_100_50_08_0_03_03(1:21)./(TTime/10^3)]; save('delay_abs.dat', 'ttt','-ascii'); ttt=[Lam,dataAver(den50_100_50_08_0_03_03),dataAver(den_del_02_50_100_50_08_0_03_03(1:21)),dataAver(den_del_01_50_100_50_08_0_03_03(1:21)),dataAver(den_del_005_50_100_50_08_0_03_03(1:21))]; save('delay_rel.dat', 'ttt','-ascii');