ohmmemit |
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% ohmmemit rrm.hmm -seed 1079460101 Extract HMM sequences HMMER hmmemit program output file [rrm.ohmmemit]: |
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Extract HMM sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile HMMER hidden markov model file [-outfile] outfile [*.ohmmemit] HMMER hmmemit program output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -seed integer [0] Random seed (Integer 0 or more) -selex boolean [N] Output in selex format -consensus boolean [N] Output consensus sequence -number integer [10] Number of sequences to produce (Any integer value) Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-infile] (Parameter 1) |
infile | HMMER hidden markov model file | Input file | Required |
[-outfile] (Parameter 2) |
outfile | HMMER hmmemit program output file | Output file | <*>.ohmmemit |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-seed | integer | Random seed | Integer 0 or more | 0 |
-selex | boolean | Output in selex format | Boolean value Yes/No | No |
-consensus | boolean | Output consensus sequence | Boolean value Yes/No | No |
-number | integer | Number of sequences to produce | Any integer value | 10 |
Associated qualifiers | ||||
"-outfile" associated outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
HMMER2.0 NAME rrm DESC LENG 72 ALPH Amino RF no CS no MAP yes COM ../src/hmmbuild -F rrm.hmm rrm.slx COM ../src/hmmcalibrate rrm.hmm NSEQ 70 DATE Wed Jul 8 08:13:25 1998 CKSUM 2768 XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 EVD -53.840649 0.214434 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -21 * -6129 1 -1234 -371 -8214 -7849 -5304 -8003 -7706 2384 -7769 2261 -681 -7660 -7694 -7521 -7816 -7346 -5543 1527 -6974 -6639 1 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12326 -894 -1115 -701 -1378 -21 * 2 -3634 -3460 -5973 -5340 3521 -2129 -4036 -831 -2054 -1257 -2663 -4822 -5229 -4557 -4735 -1979 -1569 -1476 -3893 3439 2 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12326 -894 -1115 -701 -1378 * * 3 -5570 838 -8268 -7958 -5637 -8152 -8243 2427 -7947 -461 -539 -7805 -7843 -7878 -8124 -7550 -5559 3130 -7481 -7000 3 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12326 -894 -1115 -701 -1378 * * 4 -1146 -4797 -1564 -2630 -1480 2769 -2963 -1850 992 -4812 -3887 737 -4397 -120 793 -205 -1019 -4418 -4981 -1059 4 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12326 -894 -1115 -701 -1378 * * 5 -5242 -7035 445 -3538 -7284 1773 -4583 -7166 -4676 -7046 -6312 3633 -1651 -1262 -849 -1278 -5287 -6650 -7228 -291 5 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12326 -894 -1115 -701 -1378 * * 6 -6898 -6238 -9292 -8703 -410 -9176 -7772 820 -8535 3071 -753 -8917 -8033 -7171 -7955 -8614 -6722 5 -6136 -6414 6 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 278 394 45 96 359 117 -369 -294 -249 - -33 -6025 -12326 -153 -3315 -701 -1378 * * 7 -5 -5297 178 -2982 -5685 -2278 -528 -5452 -1615 -5394 -4488 1396 3136 -3022 -3659 780 976 -4981 -5565 -4854 8 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -11 -11284 -12327 -894 -1115 -701 -1378 * * 8 -3329 -4799 -805 543 789 -4303 572 -4868 140 -1087 -3888 -603 1691 530 183 -162 293 -2124 2317 2037 9 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -12 -11284 -12327 -894 -1115 -701 -1378 * * 9 -373 -4801 2182 1353 -1426 44 -407 -1928 -366 -4817 -3891 1263 -4395 -1080 -666 295 50 -1947 -4985 397 10 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -12 -11285 -12327 -894 -1115 -701 -1378 * * 10 450 1883 -5953 -5317 -1256 -1301 -4027 1322 -1847 -283 1542 -4802 -5206 -1502 -4713 -4241 2143 1615 -3893 -3551 11 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -12 -11285 -12327 -894 -1115 -701 -1378 * * [Part of this file has been deleted for brevity] - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -17 -11290 -12332 -894 -1115 -701 -1378 * * 57 -2038 -3436 -5943 -5308 -1145 -5154 -4025 2255 423 1498 1203 -4797 -1707 -478 -1267 -2117 -3548 1450 -3893 -931 75 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -18 -11291 -12333 -894 -1115 -701 -1378 * * 58 622 -4802 1764 1486 -5123 -4302 -2961 -1060 334 -4818 -3891 -420 -4396 1293 1148 487 -3268 -1087 -4985 -429 76 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -102 -11291 -4156 -894 -1115 -701 -1378 * * 59 1265 -231 -1498 1351 -5045 -262 -355 -4796 922 -1073 -3813 778 -4318 877 -34 53 386 -2030 289 -4225 77 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -18 -11207 -12249 -894 -1115 -160 -3250 * * 60 -684 813 -5723 -473 532 -2124 -3981 -2958 -121 2114 2840 -1421 -5174 -4409 -926 -4196 -1685 -376 -3915 497 78 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -18 -11291 -12333 -894 -1115 -701 -1378 * * 61 -1812 -4803 1626 -749 -515 -1133 -415 -4875 -1294 -4819 -3892 3181 -793 1470 -1377 -246 -3268 -4425 -4986 -193 79 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -18 -11291 -12333 -894 -1115 -701 -1378 * * 62 -1812 -4808 -1465 33 -1509 2998 1583 -4879 122 -4823 -3897 972 -4400 -1078 -3055 -1613 -682 -4429 -4991 -1114 80 - -149 -500 232 43 -378 398 105 -627 212 -466 -721 275 393 45 98 359 117 -367 -295 -250 - -98 -4229 -12334 -49 -4901 -701 -1378 * * 63 -676 -4701 -742 -1422 825 -589 -545 255 1702 -2571 812 -2986 -4424 796 418 -221 1302 -1179 -4912 1028 82 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -19 -11292 -12334 -894 -1115 -701 -1378 * * 64 -3341 -4695 350 1378 -1551 -1973 -2998 477 1265 78 273 -1163 21 504 -1507 -1108 282 114 -19 473 83 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -19 -11292 -12334 -894 -1115 -701 -1378 * * 65 -3605 -3444 -949 -2090 2356 -1177 -4010 1410 -1703 1341 -404 -1673 -747 -4487 -4679 -2139 -1048 1197 -3900 411 84 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -19 -11292 -12334 -894 -1115 -701 -1378 * * 66 -655 -539 1179 279 -1324 1202 -2962 -1895 147 -682 1298 1427 -2056 608 756 -1119 -1893 -4419 -4982 140 85 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -19 -11292 -12335 -894 -1115 -701 -1378 * * 67 -1814 -4814 166 -2636 -5135 2921 -568 -4885 -1333 -2415 -3903 1495 -4406 -312 -619 602 -1672 -4436 -4997 -4314 86 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -20 -11293 -12335 -894 -1115 -701 -1378 * * 68 -3329 1217 -624 -797 -1594 -4303 1580 -4872 2069 -2414 -3890 617 -4396 283 2449 -560 -267 -2067 -4984 -1334 87 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -20 -11293 -12335 -894 -1115 -701 -1378 * * 69 108 566 -1460 747 -1608 -4306 -2965 -30 1407 -2607 -3878 346 1033 -336 863 -1038 745 617 -4975 -4296 88 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -20 -11293 -12335 -894 -1115 -701 -1378 * * 70 -1318 -3465 -283 -172 -3423 -2053 -3974 1957 -4721 1761 1425 -4678 -1762 -4391 -1578 -1974 -1561 1341 -3918 -3570 89 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -20 -11293 -12336 -894 -1115 -701 -1378 * * 71 -1165 -4790 -240 -275 -5105 -4306 1035 -2009 1665 -395 707 -1334 -218 -188 1891 -1077 -383 404 110 348 90 - -149 -500 233 43 -381 398 106 -626 210 -464 -720 275 394 45 96 359 117 -369 -294 -249 - -43 -6001 -12336 -150 -3342 -701 -1378 * * 72 -1929 1218 -1535 -1647 -3990 -4677 -3410 1725 207 -1481 -3117 -3608 -810 -1118 -743 -1942 428 2687 -4325 -3869 92 - * * * * * * * * * * * * * * * * * * * * - * * * * * * * * 0 // |
>seq1 LFIKYLTTSCTETHLKDKFANYGEVVNIDIVLDADDGQLNGFGFIIFTSH IEEQDAKKLDGKKYKGKVVES >seq2 LFVGNLHPIGRPEQLKDLFVNAYQVTQIKLLTTTTARARGYGFIEFPSHL SVTKAVAKKSGQGLSGNPVKI >seq3 IYVNGLDDDVTEDELERLLREFGLFLAFQLCKQSGKFSGMAFIEYDNSDY TQSIIRWLPGKVVMQRAITC >seq4 VYITNLPPGVQKQELFDVKDTYFGEHGPVVRFNISRDDDDTQTGEASGFG FITFEQLEDDNMAINEEAFGKLIGGKKAKV >seq5 IFVGSVTHETTESLLKLTFSKQGGVKNINNPRDDETERSRNYATVEFTTE EDAEAALENLRGIKINNRKLHI >seq6 GYVERLPEYASQKSFKNVFQKRGSIKLSKLPTIAQNRGQGFVTFSKHEQA AAALSEMNGDELEGKKISV >seq7 LYVKNLPYGVDEDKIKDAFKSEGPITVKVVLIDAASLRIHGFGFIEFPSV ADMAKAIKALEGFETFNVKIHI >seq8 LFVGGLTYFAKEEALYDLLSKFAQSEQISLANDPETGMSKGYAYVRYETE EDVDKAVENLDNIIFNGRTLRR >seq9 IFVGNIDRKITRKEFENLFAPFGPSTVFPIIRGKNTGYAFVRYDDVQNAA HLLESLDGTSDGAEVEKI >seq10 MYIGNLASDITLDDLADIFSPNVRVVSAVLLKATGHSRGFAFVEFEKEEA ATSCIANYENTEGNGHVVPV |
Program name | Description |
---|---|
ehmmalign | Align sequences to an HMM profile |
ehmmbuild | Build a profile HMM from an alignment |
ehmmcalibrate | Calibrate HMM search statistics |
ehmmconvert | Convert between profile HMM file formats |
ehmmemit | Generate sequences from a profile HMM |
ehmmfetch | Retrieve an HMM from an HMM database |
ehmmindex | Create a binary SSI index for an HMM database |
ehmmpfam | Search one or more sequences against an HMM database |
ehmmsearch | Search a sequence database with a profile HMM |
libgen | Generate discriminating elements from alignments |
ohmmalign | Align sequences with an HMM |
ohmmbuild | Build HMM |
ohmmcalibrate | Calibrate a hidden Markov model |
ohmmconvert | Convert between HMM formats |
ohmmfetch | Extract HMM from a database |
ohmmindex | Index an HMM database |
ohmmpfam | Align single sequence with an HMM |
ohmmsearch | Search sequence database with an HMM |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.