GeneMark.hmm for Prokaryotes and Low Eukaryotes (Version 2.1) (Reload this page) Reference: Lukashin A. and Borodovsky M., GeneMark.hmm: new solutions for gene finding, NAR, 1998, Vol. 26, No. 4, pp. 1107-1115. [ Download PDF ] This page has been updated to run version 2.1 of Genemark.hmm for prokaryotes, as well as version 2.4 of GeneMark. This version is significantly faster that the previous version and can analyze a sequence of 1 million base pairs in under 15 seconds. Support of prediction of overlapping genes has been vastly improved as well.0. Please note that email is the only way to receive results for sequences longer than 4 MB. This service is in a testing phase. Please report problems and offer suggestions to John Besemer . UPDATE (January 18, 2002): New models included for many newly sequenced prokaryotic genomes Listing of previous updates ------------------------------------------------------------------------ Gene Prediction Results Information on input sequence Sequence title: Mycobacterium Length: 580074 bp G+C percentage: 31.69 % Parse predicted by GeneMark.hmm 2.1 GeneMark.hmm PROKARYOTIC (Version 2.2) Model organism: Pseudonative.model Fri Jan 9 04:21:55 2004 Predicted genes Gene Strand LeftEnd RightEnd Gene Class # Length 1 + 2874 2975 102 2 2 + 8280 8372 93 2 3 + 15281 15397 117 2 4 + 26375 26428 54 1 5 + 37912 38025 114 2 6 - 45158 45223 66 2 7 + 56285 56479 195 2 8 + 62952 63059 108 2 9 - 72102 72185 84 2 10 + 79162 79941 780 2 11 + 85604 85942 339 2 12 - 86025 86102 78 2 13 + 86827 87033 207 2 14 + 89617 89823 207 2 15 + 93220 93654 435 2 16 + 94535 95782 1248 2 17 + 95783 96697 915 2 18 + 103731 104123 393 2 19 + 105106 105450 345 2 20 + 109262 109675 414 2 21 + 112390 112725 336 2 22 + 114418 114798 381 2 23 + 115873 116874 1002 2 24 + 123784 123867 84 2 25 + 132779 132964 186 2 26 + 143859 143954 96 2 27 + 149198 149359 162 1 28 + 159821 160099 279 2 29 + 167217 167555 339 2 30 + 168675 168806 132 2 31 + 169110 169292 183 2 32 + 169471 169566 96 2 33 + 173971 174117 147 2 34 - 174180 174455 276 2 35 + 175301 175396 96 2 36 + 176512 177183 672 2 37 + 177844 178278 435 2 38 + 179951 180268 318 2 39 + 181595 182866 1272 2 40 + 185828 185917 90 2 41 + 187541 187795 255 2 42 + 190408 190749 342 2 43 + 191145 191780 636 2 44 + 191784 192104 321 2 45 + 192804 192893 90 2 46 + 193934 194470 537 2 47 + 194892 195086 195 2 48 + 195755 196123 369 2 49 + 196123 196449 327 2 50 + 197179 197604 426 2 51 + 197665 198072 408 2 52 + 198167 198514 348 2 53 + 198750 199154 405 2 54 + 199690 201039 1350 2 55 + 201680 202426 747 2 56 + 202762 203019 258 2 57 + 203516 203845 330 2 58 + 204110 204502 393 2 59 + 205383 205685 303 2 60 + 206048 206596 549 2 61 - 207293 207592 300 2 62 + 213601 213936 336 2 63 + 220890 221375 486 2 64 + 222030 222533 504 2 65 + 222601 222846 246 2 66 + 223239 223361 123 2 67 + 224259 224582 324 2 68 + 224979 225905 927 2 69 + 225916 226278 363 2 70 + 226282 226458 177 2 71 + 226747 226947 201 2 72 - 227085 227291 207 2 73 + 227821 229065 1245 2 74 + 229468 229809 342 2 75 + 230766 230942 177 2 76 + 235635 236060 426 2 77 + 237845 238192 348 2 78 + 238186 239151 966 2 79 + 239247 239615 369 2 80 + 240322 242067 1746 2 81 + 242223 242510 288 2 82 - 244802 245278 477 2 83 + 250550 250795 246 2 84 + 255124 255591 468 2 85 + 255594 256457 864 2 86 - 257163 257240 78 2 87 - 257509 257748 240 2 88 - 258082 258468 387 2 89 + 259404 262328 2925 2 90 + 266665 267090 426 2 91 + 269708 270139 432 2 92 + 276874 278274 1401 2 93 + 279199 279498 300 2 94 + 279491 279805 315 2 95 + 280242 280643 402 2 96 + 283395 284372 978 2 97 + 284517 285782 1266 2 98 - 285779 285997 219 2 99 - 296111 296626 516 2 100 - 296729 297133 405 2 101 - 301041 301256 216 2 102 + 308483 309007 525 2 103 + 312844 313191 348 2 104 + 314352 314525 174 2 105 - 326028 326795 768 2 106 - 329830 330363 534 2 107 - 331483 332214 732 2 108 - 332232 332603 372 2 109 - 333336 334418 1083 2 110 - 334855 335397 543 2 111 + 338792 339754 963 2 112 - 342032 342466 435 2 113 - 343850 344098 249 2 114 - 344364 344849 486 2 115 + 349296 349619 324 2 116 - 351407 351610 204 2 117 - 356474 356569 96 2 118 - 366526 367860 1335 2 119 - 371236 371412 177 2 120 - 374978 376483 1506 2 121 - 380052 380159 108 2 122 + 390299 390394 96 2 123 + 397794 398003 210 2 124 - 401752 401907 156 2 125 - 401900 402640 741 2 126 - 403722 404189 468 2 127 - 414322 414768 447 2 128 - 424192 424350 159 2 129 + 428457 428630 174 2 130 + 428943 429125 183 2 131 + 429304 429378 75 2 132 + 429730 429900 171 2 133 - 429914 430066 153 2 134 + 430368 430556 189 2 135 - 432110 433204 1095 2 136 - 434768 435751 984 2 137 - 435944 436753 810 2 138 - 445253 445471 219 2 139 + 448797 448838 42 2 140 + 460372 460494 123 1 141 - 471533 471595 63 1 142 + 478273 478314 42 2 143 - 484947 485165 219 2 144 - 485346 485444 99 2 145 - 485682 485903 222 2 146 - 486792 486980 189 2 147 - 488322 488438 117 2 148 - 493912 494265 354 2 149 - 504313 504432 120 2 150 - 515419 515478 60 2 151 - 524746 524931 186 2 152 - 534500 534562 63 1 153 - 537645 537728 84 2 154 - 549065 549130 66 1 155 - 554428 555318 891 2 156 - 560994 561113 120 2 157 - 562071 562163 93 2 158 - 572710 572772 63 2 ------------------------------------------------------------------------ Input Sequence Title (optional): Sequence Text: Sequence File upload: Species: Typical Model Atypical Model Model Order: Output Options E-Mail Address (required for graphical output or sequences longer than 4000000 bp) Generate PDF graphics (screen) Generate PostScript graphics (email) Print GeneMark 2.4 predictions in addition to GeneMark.hmm predictions Translate predicted genes into protein Run ------------------------------------------------------------------------ Web pages maintained by GeneMark administrator, gte851w@prism.gatech.edu . Please send any suggestions for improvements or problems to the web page maintainer.