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ehmmfetch |
% ehmmfetch ../ehmmindex-keep/myhmms 7LES_DROME/1799-1891 Extract HMM from a database Output file [outfile.ehmmfetch]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-database] string Database name [-name] string Entry name [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory3 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 | |
---|---|---|---|
[-database] (Parameter 1) |
Database name | Any string is accepted | An empty string is accepted |
[-name] (Parameter 2) |
Entry name | Any string is accepted | An empty string is accepted |
[-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.ehmmfetch |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
HMMER2.0 NAME 7LES_DROME/1799-1891 ACC DESC LENG 84 ALPH Amino RF yes CS yes MAP yes COM ehmmbuild ../../data/hmm/fn3.slx fn3.hmm COM ehmmcalibrate myhmms -seed 1079460101 NSEQ 109 DATE Fri Jul 15 12:00:00 2005 CKSUM 4633 XT -8455 -4 0 * -8455 -4 0 * 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 -7.797886 0.598186 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 -13 * -6794 1 -1696 -4266 -5468 -857 -4249 -2813 -1464 -707 -2361 323 -3458 -4826 3646 -1897 -4829 -1261 -1335 -180 -4697 -1445 1 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -1013 -7375 2 -661 -5430 1594 -484 -5749 356 -3594 -5499 -1902 -454 -4519 -541 1746 -1534 -3682 1881 -218 -1175 -5614 -1565 2 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7366 3 1863 -5433 -1246 26 -5754 -787 -3592 -5505 174 -2261 -4522 -578 2069 517 -53 117 -885 -568 -5616 -1862 3 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7358 4 -933 -4330 -2306 -2375 -4321 -5548 -4342 -197 -4555 -1694 -3520 -1961 3679 -1767 -2193 -4571 -2165 1336 -4755 -4362 4 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7349 5 -1820 -5403 -2308 327 -457 168 -395 -1516 -104 -520 -384 -3583 1306 1270 1192 730 882 -1087 -5594 -1860 5 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 R -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7340 6 -982 -749 1190 -1011 -1118 1264 -288 -624 -762 -1316 -4520 2373 -1293 508 144 -1253 226 -5052 -320 -1913 6 N -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 N -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7331 7 -970 -4169 -164 -707 -29 -1178 -4516 340 -5043 1932 627 101 392 -968 -2232 -4736 -2233 1416 -4614 -4253 7 F -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 F -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7322 8 -1777 -5430 -1395 -133 -485 -1202 1638 -150 523 -314 -4519 -1070 -385 709 1029 806 906 500 -5614 -4932 8 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7313 9 1184 673 -6214 -5601 1588 -1269 -129 561 -975 -1205 -1064 -2147 -1311 219 -852 -479 57 1890 -4575 -4223 9 V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 V -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7304 10 -618 -1044 -126 168 -1034 -1670 -1237 -302 -47 -169 624 -828 -5103 -865 -727 1021 1874 314 666 -1660 10 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 [Part of this file has been deleted for brevity] V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 V -17 -11290 -12332 -894 -1115 -701 -1378 -7171 -6443 57 415 -235 151 -1692 196 -943 -3424 1368 -281 543 1497 -1265 -4765 1123 -714 -1118 -698 331 -4311 -27 57 L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 L -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6426 58 -392 -4801 1422 154 257 -976 -325 -348 1136 -182 -518 -449 -582 84 1071 -42 -259 -4422 -4984 -1114 58 D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 D -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6409 59 1019 -244 -720 268 -486 -304 -511 -857 -597 384 -3883 1880 -1432 25 -266 -599 544 -1258 -4979 -4298 59 Q -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 Q -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6392 60 -648 -361 -1645 149 -1712 -98 -2976 195 284 942 2156 1642 -1798 637 -685 -614 -1393 -4368 -4953 -253 60 K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 K -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6375 61 -495 -127 596 257 1 687 -344 -4870 388 -1674 888 2158 -252 554 -557 -1192 -645 -925 -4984 -1289 61 E -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 E -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6358 62 -1174 -4786 -513 345 -470 1975 1744 -1919 674 -976 236 503 -2145 935 -1306 -3214 -1546 -956 -4974 781 62 H -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 H -19 -11292 -12334 -894 -1115 -701 -1378 -7171 -6340 63 -666 -120 197 263 443 569 -3004 492 662 -346 -777 690 -4431 450 -205 -417 -479 105 -4895 226 63 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 R -19 -11292 -12334 -894 -1115 -701 -1378 -7171 -6322 64 -1695 -4564 90 808 321 -207 -958 170 606 -195 1319 -1668 -4468 42 233 -1958 -348 952 -101 1161 64 L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 L -19 -11248 -12290 -894 -1115 -701 -1378 -7171 -6304 65 -103 -4195 176 -803 -407 598 -3169 618 -250 684 -592 616 -392 -2836 -1348 -575 500 786 -4517 -956 65 D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 D -19 -11169 -12211 -894 -1115 -701 -1378 -7171 -6285 66 -3216 -41 863 117 14 1749 -370 -4753 -18 -877 1184 927 -1393 -238 899 -1126 -134 -1669 -4869 -1116 66 G -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 G -20 -11119 -12161 -894 -1115 -701 -1378 -7171 -6267 67 -883 -66 -1410 -539 -4946 1730 1102 -1518 1448 -2272 -346 1076 -4239 -706 -71 146 -220 -811 543 -284 67 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 R -20 -11076 -12119 -894 -1115 -701 -1378 -7171 -6248 68 -3135 -4561 -1467 -537 -307 -479 -2777 700 1697 -450 -3655 168 -4209 -801 2141 -780 -67 349 -4756 -4085 68 V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 V -20 -11004 -12046 -894 -1115 -701 -1378 -7171 -6229 69 -554 1467 -1099 262 -1323 -4214 -2905 -212 965 313 -172 -1196 916 -979 443 -902 161 1207 401 -3800 69 I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 I -20 -10946 -11988 -894 -1115 -701 -1378 -7171 -6209 70 -286 -3937 -130 157 -851 -1526 -2879 1413 133 1121 -3083 -2959 -59 -13 194 -3121 -1149 916 -4255 122 70 D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 D -21 -10829 -11871 -894 -1115 -701 -1378 -7171 -6190 71 -1515 -4363 -145 -970 -4677 -1647 -167 764 1490 -1304 418 -973 10 -592 1727 -649 -596 1115 -4551 -717 71 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -21 -10478 -11520 -894 -1115 -701 -1378 -7171 -6170 72 -1247 1262 534 -2707 -3242 -1113 -2669 654 698 -335 -2371 -2868 -791 -448 781 -2905 -104 2274 -3578 -3123 72 K * * * * * * * * * * * * * * * * * * * * K * * * * * * * -7171 0 // |
HMMER2.0 NAME 7LES_DROME/1799-1891 ACC DESC LENG 84 ALPH Amino RF yes CS yes MAP yes COM ehmmbuild ../../data/hmm/fn3.slx fn3.hmm COM ehmmcalibrate myhmms -seed 1079460101 NSEQ 109 DATE Fri Jul 15 12:00:00 2005 CKSUM 4633 XT -8455 -4 0 * -8455 -4 0 * 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 -7.797886 0.598186 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 -13 * -6794 1 -1696 -4266 -5468 -857 -4249 -2813 -1464 -707 -2361 323 -3458 -4826 3646 -1897 -4829 -1261 -1335 -180 -4697 -1445 1 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -1013 -7375 2 -661 -5430 1594 -484 -5749 356 -3594 -5499 -1902 -454 -4519 -541 1746 -1534 -3682 1881 -218 -1175 -5614 -1565 2 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7366 3 1863 -5433 -1246 26 -5754 -787 -3592 -5505 174 -2261 -4522 -578 2069 517 -53 117 -885 -568 -5616 -1862 3 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7358 4 -933 -4330 -2306 -2375 -4321 -5548 -4342 -197 -4555 -1694 -3520 -1961 3679 -1767 -2193 -4571 -2165 1336 -4755 -4362 4 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7349 5 -1820 -5403 -2308 327 -457 168 -395 -1516 -104 -520 -384 -3583 1306 1270 1192 730 882 -1087 -5594 -1860 5 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 R -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7340 6 -982 -749 1190 -1011 -1118 1264 -288 -624 -762 -1316 -4520 2373 -1293 508 144 -1253 226 -5052 -320 -1913 6 N -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 N -9 -11957 -12999 -894 -1115 -701 -1378 -7388 -7331 7 -970 -4169 -164 -707 -29 -1178 -4516 340 -5043 1932 627 101 392 -968 -2232 -4736 -2233 1416 -4614 -4253 7 F -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 F -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7322 8 -1777 -5430 -1395 -133 -485 -1202 1638 -150 523 -314 -4519 -1070 -385 709 1029 806 906 500 -5614 -4932 8 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7313 9 1184 673 -6214 -5601 1588 -1269 -129 561 -975 -1205 -1064 -2147 -1311 219 -852 -479 57 1890 -4575 -4223 9 V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 V -10 -11957 -12999 -894 -1115 -701 -1378 -7388 -7304 10 -618 -1044 -126 168 -1034 -1670 -1237 -302 -47 -169 624 -828 -5103 -865 -727 1021 1874 314 666 -1660 10 R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 [Part of this file has been deleted for brevity] L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 L -15 -11962 -13005 -894 -1115 -701 -1378 -7388 -6629 69 -645 -5232 -939 -311 -1078 -782 721 -14 -492 117 -1380 -207 -362 -823 -816 -1588 891 1565 -653 1726 69 T -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 T -15 -11963 -13005 -894 -1115 -701 -1378 -7388 -6615 70 -1242 -5312 -1984 113 120 -863 -1160 990 -1267 -1243 -1439 50 -847 -482 -53 -440 833 1161 -5528 2253 70 G -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 G -15 -11963 -13005 -894 -1115 -701 -1378 -7388 -6600 71 389 -833 -5037 -379 370 -2577 -134 648 -1 -567 -1025 121 -374 -49 -2256 -99 73 1074 -409 1922 71 I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 I -15 -11963 -13005 -894 -1115 -701 -1378 -7388 -6585 72 -627 -771 -901 -1177 -501 -530 -1293 500 -1377 -124 -1058 -592 -2238 -1896 157 537 745 1518 -353 1520 72 K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 K -16 -11949 -12991 -894 -1115 -701 -1378 -7388 -6570 73 378 -847 212 -2070 1079 -753 695 -1019 521 -1649 -344 -1083 -2171 1255 -148 -328 -460 1208 -5536 1038 73 P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 P -16 -11949 -12991 -894 -1115 -701 -1378 -7388 -6555 74 507 -5402 -797 -880 -1233 -552 -1049 142 353 108 -4493 -1060 -363 -910 1340 288 8 1131 -5590 -1612 74 G -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 G -16 -11949 -12991 -894 -1115 -701 -1378 -7388 -6539 75 277 -5371 181 -988 -138 -99 -993 163 -33 -600 -1239 21 -1212 -834 156 585 -1584 1468 -5568 766 75 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -16 -11937 -12979 -894 -1115 -701 -1378 -7388 -6524 76 381 -5386 -508 -562 -582 254 -396 -1055 -1359 -1310 -1371 897 -898 1006 773 519 83 225 -291 1066 76 G -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 G -16 -11937 -12979 -894 -1115 -701 -1378 -7388 -6508 77 822 -5403 -839 -53 -511 341 522 -39 362 -536 -4493 286 -2102 787 -117 -266 188 65 -5587 716 77 Y -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 Y -16 -11923 -12965 -894 -1115 -701 -1378 -7388 -6492 78 -199 -5391 -1182 519 -1162 281 -1208 -2420 38 -936 550 942 -1205 940 749 818 -657 134 -5575 514 78 S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 S -17 -11809 -12851 -894 -1115 -701 -1378 -7388 -6476 79 304 -5284 -326 175 -323 84 553 -861 -348 -2876 -76 1272 -636 13 946 774 -124 -94 -5468 -505 79 L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 L -17 -11721 -12763 -894 -1115 -701 -1378 -7388 -6459 80 -372 -695 -1107 704 -1874 604 -71 -329 -277 -1413 -4278 -1534 -1077 769 -106 1263 93 -537 823 1301 80 W -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 W -17 -11526 -12568 -894 -1115 -701 -1378 -7388 -6443 81 712 630 -832 129 -1696 1120 196 111 -410 -2601 164 -1425 -420 -1191 119 288 468 -54 -81 517 81 V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 V -18 -11366 -12408 -894 -1115 -701 -1378 -7388 -6426 82 412 -4862 -632 3 2 1822 -3033 -1933 -1326 -1074 -3953 7 -755 -197 -616 639 1164 -1954 -5048 -136 82 Q -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 Q -18 -11259 -12301 -894 -1115 -701 -1378 -7388 -6409 83 103 -37 -1573 717 -453 590 -307 -527 -647 -1470 -3752 517 -668 -2535 809 999 89 -180 249 499 83 A -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 A -18 -11103 -12145 -894 -1115 -701 -1378 -7388 -6392 84 -874 -4613 -1270 516 -436 1583 -196 21 -1132 -2164 -3704 224 -491 482 -1101 1177 -117 -389 406 2 84 H * * * * * * * * * * * * * * * * * * * * H * * * * * * * -7388 0 // |
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 |
ehmmemit | Extract HMM sequences |
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.