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ehmmcalibrate |
Usage:
ehmmcalibrate [options] hmmfilein hmmfileout
The hmmfileout parameter is new to EMBASSY HMMER.
hmmcalibrate reads an HMM file from
Go to the input files for this example
Example 2
Go to the input files for this example
More or less all options documented as "expert" in the original hmmer user guide are given in ACD as "advanced" options (-options must be specified on the command-line in order to be prompted for a value for them).
ehmmcalibrate reads any normal sequence USAs.
The following additional options are provided:
Please read the 'Notes' section below for a description of the differences between the original and EMBASSY HMMER, particularly which application command line options are supported.
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.
Jon Ison (jison © ebi.ac.uk)
This program is an EMBASSY wrapper to a program written by Sean Eddy as part of his hmmer package.
Please report any bugs to the EMBOSS bug team in the first instance, not to Sean Eddy.
Algorithm
Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory.
Usage
Here is a sample session with ehmmcalibrate
% ehmmcalibrate ../ehmmbuild-ex-keep/globin.hmm globino.hmm -seed 1
Calibrate HMM search statistics
hmmcalibrate -- calibrate HMM search statistics
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: ../ehmmbuild-ex-keep/globin.hmm
Length distribution mean: 350
Length distribution s.d.: 350
Number of samples: 5000
random seed: 1
histogram(s) saved to: [not saved]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM : globins50
mu : -35.959286
lambda : 0.267496
max : -8.753000
//
hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm
Go to the output files for this example
% ehmmcalibrate ../ehmmbuild-ex4-keep/myhmms myhmmso -seed 1
Calibrate HMM search statistics
hmmcalibrate -- calibrate HMM search statistics
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: ../ehmmbuild-ex4-keep/myhmms
Length distribution mean: 350
Length distribution s.d.: 350
Number of samples: 5000
random seed: 1
histogram(s) saved to: [not saved]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM : rrm
mu : -45.860321
lambda : 0.213107
max : -13.804000
//
HMM : fn3
mu : -44.960484
lambda : 0.229546
max : -12.242000
//
HMM : pkinase
mu : -193.864883
lambda : 0.143572
max : -157.132004
//
hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
Go to the output files for this example
Command line arguments
Where possible, the same command-line qualifier names and parameter order is used as in the original hmmer. There are however several unavoidable differences and these are clearly documented in the "Notes" section below.
Standard (Mandatory) qualifiers:
[-hmmfilein] infile File containing an HMM.
[-hmmfileout] outfile [*.ehmmcalibrate] File containing an HMM
with EVD parameters.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-cpu integer [0] Sets the maximum number of CPUs that the
program will run on. The default is to use
all CPUs in the machine. Overrides the HMMER
NCPU environment variable. Only affects
threaded versions of HMMER (the default on
most systems). (Integer 0 or more)
-fixed integer [0] Fix the length of the random sequences
to
Standard (Mandatory) qualifiers
Allowed values
Default
[-hmmfilein]
(Parameter 1)File containing an HMM.
Input file
Required
[-hmmfileout]
(Parameter 2)File containing an HMM with EVD parameters.
Output file
<*>.ehmmcalibrate
Additional (Optional) qualifiers
Allowed values
Default
(none)
Advanced (Unprompted) qualifiers
Allowed values
Default
-cpu
Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).
Integer 0 or more
0
-fixed
Fix the length of the random sequences to <n>, where <n> is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution.
Integer 0 or more
0
-mean
Set the mean length of the synthetic sequences to <x>, where <x> is a positive real number. The default is 350.
Any numeric value
350.0
-num
Set the number of synthetic sequences to <n>, where <n> is a positive integer. If <n> is less than about 1000, the ft to the EVD may fail. Higher numbers of <n> will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time.
Integer 0 or more
5000
-pvm
Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmcalibrate-pvm must be installed on all the PVM nodes. Optional PVM support must have been compiled into HMMER.
Boolean value Yes/No
No
-sd
Set the standard deviation of the synthetic sequence length distribution to <x>, where <x> is a positive real number. The default is 350. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0.
Number 0.000 or more
350.0
-seed
Set the random seed to <n>, where <n> is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM.
Integer 0 or more
0
-histfile
Save a histogram of the scores and the fitted theoretical curve to file.
Output file
<*>.ehmmcalibrate
Input file format
Alignment and sequence formats
Input and output of alignments and sequences is limited to the formats that the original hmmer supports. These include stockholm, SELEX, MSF, Clustal, Phylip and A2M /aligned FASTA (alignments) and FASTA, GENBANK, EMBL, GCG, PIR (sequences). It would be fairly straightforward to adapt the code to support all EMBOSS-supported formats.
Compressed input files
Automatic processing of gzipped files is not supported.
Input files for usage example
File: ../ehmmbuild-ex-keep/globin.hmm
HMMER2.0 [2.3.2]
NAME globins50
LENG 143
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf
NSEQ 50
DATE Sun Jul 15 12:00:00 2007
CKSUM 9858
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
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
-450 * -1900
1 591 -1587 159 1351 -1874 -201 151 -1600 998 -1591 -693 389 -1272 595 42 -31 27 -693 -1797 -1134 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 -450 *
2 -926 -2616 2221 2269 -2845 -1178 -325 -2678 -300 -2596 -1810 220 -1592 939 -974 -671 -939 -2204 -2785 -1925 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
3 -638 -1715 -680 497 -2043 -1540 23 -1671 2380 -1641 -840 -222 -1595 437 1040 -564 -523 -1363 2124 -1313 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
4 829 -1571 -37 660 -1856 -873 152 -1578 894 -1573 -678 769 -1273 1284 58 224 447 -1175 -1782 -1125 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
5 369 -433 -475 286 -974 -1312 -19 -412 664 398 406 1030 -1394 388 -214 -261 85 -166 -1227 -725 18
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
6 -1291 -884 -3696 -3261 -1137 -3425 -2802 2322 -3066 111 19 -3028 -3275 -2855 -3100 -2670 -1269 2738 -2450 -2062 19
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
7 157 -413 -236 316 -1387 -1231 89 -863 1084 -431 -348 910 -1319 635 297 15 704 -483 -1497 -922 20
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
8 770 -1431 -43 459 -1751 -340 78 -1449 440 -1497 -631 866 -1302 825 -51 953 364 -1076 -1750 -1121 21
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
9 420 -186 -2172 -1577 8 -1818 -694 1477 -1281 760 614 -1299 -1867 -1001 -1262 -189 -12 1401 -722 -364 22
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
10 -961 -879 -2277 -1821 1366 -2213 -204 -399 -1500 -130 -39 -1427 -2266 -1186 -1511 -159 -913 -367 4721 1177 23
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
11 -48 -1782 809 844 -2073 1456 8 -1811 315 -1803 -932 180 -1365 921 -218 173 -115 -1399 -2018 -1327 24
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -68 -6528 -4832 -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
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
128 -415 -1926 1575 1399 -2219 -1163 17 -1983 527 -1929 -1039 341 -1367 1597 -212 257 -222 -1536 -2109 -1387 144
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
129 -529 -1434 -629 -143 -1926 -626 -171 -1460 2679 -1597 -839 -309 -1599 207 317 -530 -510 -130 -1840 -1369 145
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
130 811 -397 -2389 -1807 1883 -2039 -907 594 -1512 1077 687 -1532 -2065 -1201 -1483 -1125 -465 1067 -843 -472 146
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
131 -241 -102 -2327 -1710 724 -1767 -616 650 -1363 1074 1765 -718 -1809 -1026 -1252 -842 -181 1331 -541 695 147
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
132 723 95 385 823 -1820 -1168 167 -1540 875 -1362 -644 320 -1261 810 246 693 -67 -1141 -1753 -1098 148
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
133 551 -430 -1049 -481 -442 469 -241 465 -313 133 947 -411 -1543 197 -587 -146 202 522 -843 -429 149
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
134 -1086 -777 -3351 -2800 816 -2898 -1861 1501 -2515 1149 586 -2483 -2775 -2108 -2400 -2046 -1030 2380 -1511 -1216 150
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
135 1393 1409 -876 -345 -997 -525 -315 -590 -198 -847 -109 -420 -1441 -97 412 766 -130 139 -1306 -858 151
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
136 98 -1299 36 365 -1495 -1211 1241 -404 523 -952 -426 1174 -1303 511 -18 347 882 -853 -1566 -970 152
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
137 1308 -787 564 -132 -966 -1332 -203 -362 -49 -395 -57 -305 -1481 49 -437 -190 -182 1020 -1282 -802 153
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
138 -1746 -1358 -3897 -3341 -216 -3621 -2478 1774 -3040 2442 1158 -3189 -3229 -2422 -2853 -2824 -1659 392 -1720 -1647 154
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
139 1176 -1289 -179 534 -1606 -607 34 -1278 734 -1372 -534 44 -1325 433 -89 521 826 -941 -1666 -1072 155
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
140 602 -1500 -135 850 -1753 -1214 1951 -1452 838 -1484 431 118 -1306 555 347 489 -153 -1085 -1723 -1092 156
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -22 -6602 -7644 -894 -1115 -701 -1378 * *
141 351 -1646 -165 546 -1976 -498 46 -1667 2193 -1662 -798 35 -1405 476 311 -73 -306 -1287 -1859 -1254 157
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6561 -7603 -894 -1115 -701 -1378 * *
142 -1995 -1606 -3095 -2870 1739 -3015 -98 -1012 -2520 -730 655 -1990 -2962 -1884 -2326 -2167 -1915 -1128 548 4089 158
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -25 -6455 -7497 -894 -1115 -701 -1378 * *
143 -253 -1373 -267 301 -911 -565 1956 -450 1188 -1330 -497 33 -1352 502 1358 -205 -184 -941 -1604 -1026 159
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Input files for usage example 2
File: ../ehmmbuild-ex4-keep/myhmms
HMMER2.0 [2.3.2]
NAME rrm
LENG 77
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/rrm.sto
NSEQ 90
DATE Sun Jul 15 12:00:00 2007
CKSUM 8325
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
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
-16 * -6492
1 -1084 390 -8597 -8255 -5793 -8424 -8268 2395 -8202 2081 -1197 -8080 -8115 -8020 -8297 -7789 -5911 1827 -7525 -7140 1
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 -16 *
2 -2140 -3785 -6293 -2251 3226 -2495 -727 -638 -2421 -545 -675 -5146 -5554 -4879 -1183 -2536 -1928 267 76 3171 2
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
3 -2542 458 -8584 -8273 -6055 -8452 -8531 2304 -8255 -324 101 -8104 -8170 -8221 -8440 -7840 -5878 3145 -7857 -7333 3
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
4 -1505 -5144 -1922 -558 -1842 2472 -3303 -2213 1099 -5160 -4233 372 -4738 -530 1147 168 498 -4766 -5327 -1476 4
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
5 -3724 -5184 300 -3013 -1655 1803 -3353 -5245 -1569 -2686 -4276 3495 -1963 -1331 -1054 -1472 -3664 -4803 -5369 -2 5
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
6 -1569 -6106 -8967 -8363 555 -8531 -7279 654 -8092 2953 -94 -8220 -7908 -1643 -7682 -7771 -6460 -59 -6191 -6284 6
- -151 -504 230 45 -380 399 101 -621 211 -470 -713 278 399 48 91 360 113 -364 -299 -254
- -178 -3113 -12684 -1600 -578 -701 -1378 * *
7 -409 -5130 -215 -2987 -1709 -956 690 -5188 -395 -5144 -4224 729 3054 -2862 -3409 354 1293 -1381 -5321 -4644 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
8 -3674 -5118 -1004 639 420 -4652 176 -2050 404 -1039 -935 16 1755 168 147 -275 198 -1472 1889 1977 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
9 -408 -5134 2415 1299 -950 -66 -767 -1296 -2889 -1843 -4224 1084 -968 -1439 -1854 540 -314 -2304 -5320 -60 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
10 586 1804 -6294 -631 -1627 -1671 -4374 1029 -2223 -162 1172 -5147 -5554 -1870 -5058 -2327 1741 1687 -4242 687 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
11 -2134 -5144 845 -1187 -1652 -1667 -3303 -5216 -513 -801 -4233 1026 -1873 -543 -619 575 2956 -4766 -5327 -4644 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -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
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
279 -7207 -7306 -8076 -6588 -8459 -7223 -5448 -7982 -1500 -7531 -6953 -6369 -7277 -5081 4236 -7139 -6862 -7777 -7053 -7277 454
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
280 -694 -163 -5922 -5286 -1204 -2048 -610 1082 -1800 1434 -2618 -4776 2951 -4509 -4688 -1216 -1648 -2829 202 21 455
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -3168 -11253 -171 -894 -1115 -701 -1378 * *
281 -1412 -2132 -2007 -2293 -4366 3113 -2847 -4225 -3107 -4377 -3503 1660 -2881 -2661 -3396 961 -1821 -3134 -4516 -4119 456
- -150 -489 232 42 -382 400 104 -627 211 -465 -722 274 393 51 95 359 116 -370 -296 -245
- -2121 -637 -2975 -831 -1191 -6099 -21 * *
282 -968 -1818 -1787 -1351 -3112 953 -1494 -2818 -1122 -2911 -2044 -1365 -2340 -1133 1510 1816 2121 -2205 -3137 -2649 459
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -228 -7899 -2816 -894 -1115 -4964 -47 * *
283 840 -1663 -994 969 1159 503 -604 -1413 -325 -1594 -814 -688 -1996 -267 1103 -851 -755 -1179 2900 -1437 460
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -9 -7938 -8980 -894 -1115 -89 -4060 * *
284 -3257 -4642 -697 -2590 -1218 -252 -2907 -4655 -1306 -2353 -529 482 -1607 -2459 -1398 2112 2745 -4246 -4848 -4187 461
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11183 -12226 -894 -1115 -186 -3045 * *
285 2163 763 -1619 -5296 2250 -2060 -4007 1241 -4891 -489 484 -4781 -226 -4515 -4692 -678 -1688 -813 264 -3530 462
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
286 -268 -329 -158 917 -541 -1990 350 -4851 1273 -1075 388 -1130 233 840 993 -602 801 -595 -4964 -857 463
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
287 109 -243 672 2304 -5103 -4283 488 -4854 -1317 -2269 -656 -492 -1519 2679 -655 -618 -3248 -4404 -4965 -1114 464
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
288 1312 1294 -6215 -5593 -206 -1244 -4339 2188 -5201 1409 395 -5091 -5478 -4828 -5009 -4538 -3794 1162 -4188 -3846 465
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -11253 -6022 -894 -1115 -701 -1378 * *
289 -3562 799 -5767 -2054 -1235 -2075 318 138 237 2164 1713 -1454 -5145 -1272 -730 -4172 -1640 1071 -3865 -34 466
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -1470 -646 * *
290 73 1351 -674 1236 -1549 -2008 1350 -4834 1049 -2498 -3851 1801 -4356 1813 -115 -223 -1582 -1052 -4945 -4262 467
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -369 -2147 * *
291 -1739 -320 777 -2654 -1419 -2051 4360 -4707 -1358 -2412 -689 -1300 -4399 -224 537 531 -289 -2010 -4905 -1057 468
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
292 -3345 -4494 -233 -332 -563 -1986 -3051 333 99 1063 -3616 -3072 2953 -1026 -1490 -943 -1528 -1070 -4753 -4151 469
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10815 -11857 -894 -1115 -701 -1378 * *
293 -6409 -5751 -7614 -7636 2593 -7311 -4003 -5084 -7219 -150 -151 -6210 -7172 -849 -6723 -6510 -6299 -1387 4881 2807 470
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10749 -11791 -894 -1115 -701 -1378 * *
294 -4057 -3817 -6415 -5791 3203 -1638 -4541 1679 -5412 765 1434 -5333 -5617 -4930 -5182 -4791 -3987 1226 750 -3959 471
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Output file format
ehmmcalibrate
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
Output files for usage example
File: globino.hmm
HMMER2.0 [2.3.2]
NAME globins50
LENG 143
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf
COM hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm
NSEQ 50
DATE Sun Jul 15 12:00:00 2007
CKSUM 9858
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 -35.959286 0.267496
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
-450 * -1900
1 591 -1587 159 1351 -1874 -201 151 -1600 998 -1591 -693 389 -1272 595 42 -31 27 -693 -1797 -1134 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 -450 *
2 -926 -2616 2221 2269 -2845 -1178 -325 -2678 -300 -2596 -1810 220 -1592 939 -974 -671 -939 -2204 -2785 -1925 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
3 -638 -1715 -680 497 -2043 -1540 23 -1671 2380 -1641 -840 -222 -1595 437 1040 -564 -523 -1363 2124 -1313 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
4 829 -1571 -37 660 -1856 -873 152 -1578 894 -1573 -678 769 -1273 1284 58 224 447 -1175 -1782 -1125 17
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
5 369 -433 -475 286 -974 -1312 -19 -412 664 398 406 1030 -1394 388 -214 -261 85 -166 -1227 -725 18
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
6 -1291 -884 -3696 -3261 -1137 -3425 -2802 2322 -3066 111 19 -3028 -3275 -2855 -3100 -2670 -1269 2738 -2450 -2062 19
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
7 157 -413 -236 316 -1387 -1231 89 -863 1084 -431 -348 910 -1319 635 297 15 704 -483 -1497 -922 20
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
8 770 -1431 -43 459 -1751 -340 78 -1449 440 -1497 -631 866 -1302 825 -51 953 364 -1076 -1750 -1121 21
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
9 420 -186 -2172 -1577 8 -1818 -694 1477 -1281 760 614 -1299 -1867 -1001 -1262 -189 -12 1401 -722 -364 22
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
10 -961 -879 -2277 -1821 1366 -2213 -204 -399 -1500 -130 -39 -1427 -2266 -1186 -1511 -159 -913 -367 4721 1177 23
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
11 -48 -1782 809 844 -2073 1456 8 -1811 315 -1803 -932 180 -1365 921 -218 173 -115 -1399 -2018 -1327 24
[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
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
128 -415 -1926 1575 1399 -2219 -1163 17 -1983 527 -1929 -1039 341 -1367 1597 -212 257 -222 -1536 -2109 -1387 144
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
129 -529 -1434 -629 -143 -1926 -626 -171 -1460 2679 -1597 -839 -309 -1599 207 317 -530 -510 -130 -1840 -1369 145
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
130 811 -397 -2389 -1807 1883 -2039 -907 594 -1512 1077 687 -1532 -2065 -1201 -1483 -1125 -465 1067 -843 -472 146
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
131 -241 -102 -2327 -1710 724 -1767 -616 650 -1363 1074 1765 -718 -1809 -1026 -1252 -842 -181 1331 -541 695 147
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
132 723 95 385 823 -1820 -1168 167 -1540 875 -1362 -644 320 -1261 810 246 693 -67 -1141 -1753 -1098 148
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
133 551 -430 -1049 -481 -442 469 -241 465 -313 133 947 -411 -1543 197 -587 -146 202 522 -843 -429 149
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
134 -1086 -777 -3351 -2800 816 -2898 -1861 1501 -2515 1149 586 -2483 -2775 -2108 -2400 -2046 -1030 2380 -1511 -1216 150
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
135 1393 1409 -876 -345 -997 -525 -315 -590 -198 -847 -109 -420 -1441 -97 412 766 -130 139 -1306 -858 151
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
136 98 -1299 36 365 -1495 -1211 1241 -404 523 -952 -426 1174 -1303 511 -18 347 882 -853 -1566 -970 152
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
137 1308 -787 564 -132 -966 -1332 -203 -362 -49 -395 -57 -305 -1481 49 -437 -190 -182 1020 -1282 -802 153
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
138 -1746 -1358 -3897 -3341 -216 -3621 -2478 1774 -3040 2442 1158 -3189 -3229 -2422 -2853 -2824 -1659 392 -1720 -1647 154
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
139 1176 -1289 -179 534 -1606 -607 34 -1278 734 -1372 -534 44 -1325 433 -89 521 826 -941 -1666 -1072 155
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6528 -7571 -894 -1115 -701 -1378 * *
140 602 -1500 -135 850 -1753 -1214 1951 -1452 838 -1484 431 118 -1306 555 347 489 -153 -1085 -1723 -1092 156
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -22 -6602 -7644 -894 -1115 -701 -1378 * *
141 351 -1646 -165 546 -1976 -498 46 -1667 2193 -1662 -798 35 -1405 476 311 -73 -306 -1287 -1859 -1254 157
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -6561 -7603 -894 -1115 -701 -1378 * *
142 -1995 -1606 -3095 -2870 1739 -3015 -98 -1012 -2520 -730 655 -1990 -2962 -1884 -2326 -2167 -1915 -1128 548 4089 158
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -25 -6455 -7497 -894 -1115 -701 -1378 * *
143 -253 -1373 -267 301 -911 -565 1956 -450 1188 -1330 -497 33 -1352 502 1358 -205 -184 -941 -1604 -1026 159
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Output files for usage example 2
File: myhmmso
HMMER2.0 [2.3.2]
NAME rrm
LENG 77
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/rrm.sto
COM hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ 90
DATE Sun Jul 15 12:00:00 2007
CKSUM 8325
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 -45.860321 0.213107
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
-16 * -6492
1 -1084 390 -8597 -8255 -5793 -8424 -8268 2395 -8202 2081 -1197 -8080 -8115 -8020 -8297 -7789 -5911 1827 -7525 -7140 1
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 -16 *
2 -2140 -3785 -6293 -2251 3226 -2495 -727 -638 -2421 -545 -675 -5146 -5554 -4879 -1183 -2536 -1928 267 76 3171 2
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
3 -2542 458 -8584 -8273 -6055 -8452 -8531 2304 -8255 -324 101 -8104 -8170 -8221 -8440 -7840 -5878 3145 -7857 -7333 3
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
4 -1505 -5144 -1922 -558 -1842 2472 -3303 -2213 1099 -5160 -4233 372 -4738 -530 1147 168 498 -4766 -5327 -1476 4
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
5 -3724 -5184 300 -3013 -1655 1803 -3353 -5245 -1569 -2686 -4276 3495 -1963 -1331 -1054 -1472 -3664 -4803 -5369 -2 5
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
6 -1569 -6106 -8967 -8363 555 -8531 -7279 654 -8092 2953 -94 -8220 -7908 -1643 -7682 -7771 -6460 -59 -6191 -6284 6
- -151 -504 230 45 -380 399 101 -621 211 -470 -713 278 399 48 91 360 113 -364 -299 -254
- -178 -3113 -12684 -1600 -578 -701 -1378 * *
7 -409 -5130 -215 -2987 -1709 -956 690 -5188 -395 -5144 -4224 729 3054 -2862 -3409 354 1293 -1381 -5321 -4644 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
8 -3674 -5118 -1004 639 420 -4652 176 -2050 404 -1039 -935 16 1755 168 147 -275 198 -1472 1889 1977 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
9 -408 -5134 2415 1299 -950 -66 -767 -1296 -2889 -1843 -4224 1084 -968 -1439 -1854 540 -314 -2304 -5320 -60 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
10 586 1804 -6294 -631 -1627 -1671 -4374 1029 -2223 -162 1172 -5147 -5554 -1870 -5058 -2327 1741 1687 -4242 687 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
11 -2134 -5144 845 -1187 -1652 -1667 -3303 -5216 -513 -801 -4233 1026 -1873 -543 -619 575 2956 -4766 -5327 -4644 17
[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
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
279 -7207 -7306 -8076 -6588 -8459 -7223 -5448 -7982 -1500 -7531 -6953 -6369 -7277 -5081 4236 -7139 -6862 -7777 -7053 -7277 454
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
280 -694 -163 -5922 -5286 -1204 -2048 -610 1082 -1800 1434 -2618 -4776 2951 -4509 -4688 -1216 -1648 -2829 202 21 455
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -3168 -11253 -171 -894 -1115 -701 -1378 * *
281 -1412 -2132 -2007 -2293 -4366 3113 -2847 -4225 -3107 -4377 -3503 1660 -2881 -2661 -3396 961 -1821 -3134 -4516 -4119 456
- -150 -489 232 42 -382 400 104 -627 211 -465 -722 274 393 51 95 359 116 -370 -296 -245
- -2121 -637 -2975 -831 -1191 -6099 -21 * *
282 -968 -1818 -1787 -1351 -3112 953 -1494 -2818 -1122 -2911 -2044 -1365 -2340 -1133 1510 1816 2121 -2205 -3137 -2649 459
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -228 -7899 -2816 -894 -1115 -4964 -47 * *
283 840 -1663 -994 969 1159 503 -604 -1413 -325 -1594 -814 -688 -1996 -267 1103 -851 -755 -1179 2900 -1437 460
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -9 -7938 -8980 -894 -1115 -89 -4060 * *
284 -3257 -4642 -697 -2590 -1218 -252 -2907 -4655 -1306 -2353 -529 482 -1607 -2459 -1398 2112 2745 -4246 -4848 -4187 461
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11183 -12226 -894 -1115 -186 -3045 * *
285 2163 763 -1619 -5296 2250 -2060 -4007 1241 -4891 -489 484 -4781 -226 -4515 -4692 -678 -1688 -813 264 -3530 462
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
286 -268 -329 -158 917 -541 -1990 350 -4851 1273 -1075 388 -1130 233 840 993 -602 801 -595 -4964 -857 463
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
287 109 -243 672 2304 -5103 -4283 488 -4854 -1317 -2269 -656 -492 -1519 2679 -655 -618 -3248 -4404 -4965 -1114 464
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
288 1312 1294 -6215 -5593 -206 -1244 -4339 2188 -5201 1409 395 -5091 -5478 -4828 -5009 -4538 -3794 1162 -4188 -3846 465
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -11253 -6022 -894 -1115 -701 -1378 * *
289 -3562 799 -5767 -2054 -1235 -2075 318 138 237 2164 1713 -1454 -5145 -1272 -730 -4172 -1640 1071 -3865 -34 466
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -1470 -646 * *
290 73 1351 -674 1236 -1549 -2008 1350 -4834 1049 -2498 -3851 1801 -4356 1813 -115 -223 -1582 -1052 -4945 -4262 467
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -369 -2147 * *
291 -1739 -320 777 -2654 -1419 -2051 4360 -4707 -1358 -2412 -689 -1300 -4399 -224 537 531 -289 -2010 -4905 -1057 468
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
292 -3345 -4494 -233 -332 -563 -1986 -3051 333 99 1063 -3616 -3072 2953 -1026 -1490 -943 -1528 -1070 -4753 -4151 469
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10815 -11857 -894 -1115 -701 -1378 * *
293 -6409 -5751 -7614 -7636 2593 -7311 -4003 -5084 -7219 -150 -151 -6210 -7172 -849 -6723 -6510 -6299 -1387 4881 2807 470
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10749 -11791 -894 -1115 -701 -1378 * *
294 -4057 -3817 -6415 -5791 3203 -1638 -4541 1679 -5412 765 1434 -5333 -5617 -4930 -5182 -4791 -3987 1226 750 -3959 471
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Data files
None.
Notes
1. Command-line arguments
The following original HMMER options are not supported:
-h : Use -help to get help information instead.
-hmmfileout: Output file with HMM and EVD parameters.
2. Installing EMBASSY HMMER
The EMBASSY HMMER package contains "wrapper" applications providing an EMBOSS-style interface to the applications in the original HMMER package version 2.3.2 developed by Sean Eddy. Please read the file INSTALL in the EMBASSY HMMER package distribution for installation instructions.
3. Installing original HMMER
To use EMBASSY HMMER, you will first need to download and install the original HMMER package. Please read the file 00README in the the original HMMER package distribution for installation instructions:
WWW home: http://hmmer.wustl.edu/
Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
4. Setting up HMMER
For the EMBASSY HMMER package to work, the directory containing the original HMMER executables *must* be in your path. For example if you executables were installed to "/usr/local/hmmer/bin", then type:
set path=(/usr/local/hmmer/bin/ $path)
rehash
5. Getting help
Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory. The first 3 chapters (Introduction, Installation and Tutorial) are particularly useful.
References
None.
Warnings
Types of input data
hmmer v3.2.1 and therefore EMBASSY HMMER is only recommended for use with protein sequences. If you provide a non-protein sequence you will be reprompted for a protein sequence. To accept nucleic acid sequences you must replace instances of < type: "protein" > in the application ACD files with Environment variables
The original hmmer uses BLAST environment variables (below), if defined, to locate files. The EMBASSY HMMER does not.
BLASTDB location of sequence databases to be searched
BLASMAT location of substitution matrices
HMMERDB location of HMMs
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name
Description
ehmmalign
Align sequences to an HMM profile
ehmmbuild
Build a profile HMM from an alignment
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
oalistat
Statistics for multiple alignment files
ohmmalign
Align sequences with an HMM
ohmmbuild
Build HMM
ohmmcalibrate
Calibrate a hidden Markov model
ohmmconvert
Convert between HMM formats
ohmmemit
Extract HMM sequences
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
Author(s)
This program is an EMBOSS conversion of a program written by Sean Eddy
as part of his HMMER package.
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.