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ehmmemit |
% ehmmemit rrm.hmm -seed 1079460101 Extract HMM sequences Output file [rrm.ehmmemit]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-infile] infile HMM file [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -seed integer Random seed -selex boolean Output in selex format -consensus boolean Output consensus sequence -number integer Number of sequences to produce Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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. 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
HMM file | Input file | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.ehmmemit |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-seed | Random seed | Integer 0 or more | 0 |
-selex | Output in selex format | Boolean value Yes/No | No |
-consensus | Output consensus sequence | Boolean value Yes/No | No |
-number | Number of sequences to produce | Any integer value | 10 |
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 |
---|---|
ealistat | Statistics for multiple alignment files |
ehmmalign | Align sequences with an HMM |
ehmmbuild | Build HMM |
ehmmcalibrate | Calibrate a hidden Markov model |
ehmmconvert | Convert between HMM formats |
ehmmfetch | Extract HMM from a database |
ehmmindex | Index an HMM database |
ehmmpfam | Align single sequence with an HMM |
ehmmsearch | Search sequence database with an HMM |
Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.
Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.