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ehmmfetch |
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Usage:
ehmmfetch [options] database name outfile
The outfile parameter is new to EMBASSY HMMER.
hmmfetch is a small utility that retrieves an HMM called of a given name
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).
ehmmfetch 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 ehmmfetch
% ehmmfetch ../ehmmindex-ex-keep/myhmmso pkinase pkinase.ehmmfetch
Retrieve an HMM from an HMM database.
hmmfetch ../ehmmindex-ex-keep/myhmmso pkinase > pkinase.ehmmfetch
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:
[-database] infile HMMER hmm database file
[-name] string Entry name (Any string is accepted)
[-outfile] outfile [*.ehmmfetch] HMMER hidden markov model
output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-nhmm boolean Interpret name as an HMM number instead of a
name. Numbering starts at 0. For example,
to fetch the frst HMM from an HMM database
called foo, you would do 'hmmfetch -n 0
foo'.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory3 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. 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
Standard (Mandatory) qualifiers
Allowed values
Default
[-database]
(Parameter 1)HMMER hmm database file
Input file
Required
[-name]
(Parameter 2)Entry name
Any string is accepted
An empty string is accepted
[-outfile]
(Parameter 3)HMMER hidden markov model output file
Output file
<*>.ehmmfetch
Additional (Optional) qualifiers
Allowed values
Default
(none)
Advanced (Unprompted) qualifiers
Allowed values
Default
-nhmm
Interpret name as an HMM number instead of a name. Numbering starts at 0. For example, to fetch the frst HMM from an HMM database called foo, you would do 'hmmfetch -n 0 foo'.
Boolean value Yes/No
No
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: ../ehmmindex-ex-keep/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 Tue Jul 15 12:00:00 2008
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
//
Output file format
ehmmfetch
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
Output files for usage example
File: pkinase.ehmmfetch
HMMER2.0 [2.3.2]
NAME pkinase
ACC PF00069
DESC Protein kinase domain
LENG 294
ALPH Amino
RF no
CS no
MAP yes
COM hmmbuild -n pkinase --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/pkinase.sto
COM hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ 67
DATE Tue Jul 15 12:00:00 2008
CKSUM 4536
GA -57.9 -57.9
TC -57.7 -57.7
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 -193.864883 0.143572
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 * -6109
1 -3588 -3415 -5932 -2068 2209 -1198 -4007 1029 -4891 889 -2618 -4781 -5186 -4515 -1612 -2029 -1657 -333 1774 3270 1
- -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 -21 *
2 -1103 -137 -1497 1525 -5095 -4284 1704 -69 423 -1097 -3867 -503 -4377 1172 1017 -1013 975 769 -4962 -4280 2
- -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 * *
3 -3460 -131 -785 -393 1050 -4703 -3447 1378 306 1185 -596 -562 -1734 -284 173 -1848 58 960 -4250 -1088 3
- -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 * *
4 -3367 -4343 -251 -58 -1421 1411 919 542 574 989 -604 -23 -4523 -994 -3271 -1049 -1512 847 -4637 -148 4
- -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 * *
5 -1098 -4782 -183 1680 -5103 503 -434 -4854 1124 -4798 -647 -1288 -1568 1359 1836 -240 -1526 -1059 97 -4283 5
- -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 * *
6 -1811 -238 -680 526 -557 -4309 481 726 1770 -409 -3794 -2960 209 272 290 -1047 576 765 -4901 -4244 6
- -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 * *
7 -6084 -5527 -8663 -8230 -4683 -8506 -7801 2582 -2005 2411 -444 -8189 -7866 -7357 -7914 -7892 -6017 898 -6516 -6551 7
- -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 * *
8 -1162 -4907 -7014 -7375 -7618 3734 -6813 -7450 -7402 -7698 -6730 -5890 -5975 -453 -7118 -4539 -1742 -6121 -7823 -7778 8
- -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 * *
9 21 -4782 -1460 1735 -1488 -2091 -2941 -1034 378 -4798 -702 -451 -1594 1320 1488 1403 -804 -2034 -4965 -4282 9
- -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 * *
[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.
-n : Use -nhmm instead (-n causes problems for GUI developers)
-outfile : Output file with HMM.
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
ehmmcalibrate
Calibrate HMM search statistics
ehmmconvert
Convert between profile HMM file formats
ehmmemit
Generate sequences from a profile HMM
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.