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ehmmconvert |
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Usage:
ehmmconvert [options] oldhmmfile newhmmfile
hmmconvert reads an HMM file
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).
ehmmconvert reads any normal sequence USAs.
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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Jon Ison
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
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 ehmmconvert
% ehmmconvert ../ehmmcalibrate-ex-keep/globino.hmm globino.ehmmconvert -format G
Convert between profile HMM file formats
hmmconvert - convert between profile HMM file formats
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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Input HMM file: ../ehmmcalibrate-ex-keep/globino.hmm
Output HMM file: globino.ehmmconvert
Converting to: GCG Profile .prf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- converted globins50
1 HMM(s) converted and written to globino.ehmmconvert
/shared/software/bin/hmmconvert -p -F ../ehmmcalibrate-ex-keep/globino.hmm globino.ehmmconvert
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.
Convert between profile HMM file formats
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-oldhmmfile] infile HMM input file
-format menu [A] Select format (Values: A (ascii); B
(binary); G (gcg); X (xsw))
[-newhmmfile] outfile [*.ehmmconvert] HMM output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-newhmmfile" 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
[-oldhmmfile]
(Parameter 1)infile
HMM input file
Input file
Required
-format
list
Select format
A (ascii) B (binary) G (gcg) X (xsw) A
[-newhmmfile]
(Parameter 2)outfile
HMM output file
Output file
<*>.ehmmconvert
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-newhmmfile" associated outfile qualifiers
-odirectory2
-odirectory_newhmmfilestring
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
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: ../ehmmcalibrate-ex-keep/globino.hmm
HMMER2.0 [2.3.2]
NAME globins50
LENG 143
ALPH Amino
RF no
CS no
MAP yes
COM /shared/software/bin/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 /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm
NSEQ 50
DATE Fri Jul 15 12:00:00 2011
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 1157 -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 file format
ehmmconvert
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
Output files for usage example
File: globino.ehmmconvert
!!AA_PROFILE 1.0
(Peptide) HMMCONVERT v2.3.2 Length: 143 globins50||
Profile converted from a profile HMM using HMMER v2.3.2 emulation.
Use -nonor -noave -gap=10 -len=1 with profilesearch and friends
to get the closest approximation to HMMER bit scores.
WARNING: There is a loss of information in this conversion.
Neither the scores nor even the rank order of hits will be precisely
preserved in a comparison of HMMER hmmsearch to GCG profilesearch.
The profile score is an approximation of the (single-hit) HMMER score.
Cons A C D E F G H I K L M N P Q R S T V W Y U B Z X Gap Len ..
E 57 -160 14 133 -189 -22 13 -161 97 -161 -71 37 -129 57 2 -5 0 -71 -181 -115 -5 24 103 -31 100 100
E -94 -263 220 225 -286 -119 -34 -269 -31 -261 -182 20 -161 92 -99 -69 -95 -222 -280 -194 -68 128 173 -95 62 111
K -65 -173 -69 47 -206 -155 0 -169 236 -166 -85 -24 -161 41 102 -58 -54 -138 210 -133 -58 -48 45 -60 62 111
A 81 -159 -5 64 -187 -89 13 -159 87 -159 -69 75 -129 126 3 20 42 -119 -180 -114 20 31 88 -34 62 111
L 35 -45 -49 26 -99 -133 -3 -43 64 37 38 101 -141 36 -23 -28 6 -18 -124 -74 -27 19 30 -15 62 111
V -131 -90 -371 -328 -115 -344 -282 230 -308 9 0 -304 -329 -287 -311 -268 -128 271 -246 -208 -268 -340 -312 -167 62 111
K 13 -43 -25 29 -140 -125 7 -88 106 -45 -36 89 -133 61 27 0 68 -50 -151 -94 0 27 42 -20 62 111
S 75 -145 -6 44 -177 -35 5 -146 42 -151 -65 84 -132 80 -7 93 34 -109 -176 -114 93 35 58 -29 62 111
V 40 -20 -219 -159 -1 -183 -71 145 -130 74 59 -131 -188 -102 -128 -20 -3 138 -74 -38 -20 -178 -137 -45 62 111
W -98 -89 -229 -184 134 -223 -22 -41 -151 -14 -5 -144 -228 -120 -153 -17 -93 -38 470 115 -17 -190 -159 -86 62 111
! 11
G -11 -184 74 78 -213 139 -5 -187 25 -186 -99 11 -142 85 -28 10 -17 -146 -208 -139 10 45 81 -44 62 111
K -9 -131 -59 0 -149 -144 22 -36 236 -83 -46 -20 -152 33 30 -44 -36 -83 -154 -105 -44 -41 13 -40 62 111
V -147 -115 -377 -323 12 -333 -235 148 -296 10 33 -292 -322 -260 -287 -248 -142 208 -205 -174 -248 -338 -298 -163 62 111
E 8 -124 -6 99 -144 9 18 -111 85 -88 -37 17 -122 59 7 16 4 -80 -150 -2 16 4 83 -18 58 111
K 30 -118 -10 42 -141 30 17 -107 75 -118 21 15 -64 100 6 28 8 -76 -148 -89 28 1 65 -18 58 111
N -22 -189 139 51 -218 -119 182 -194 54 -189 -101 177 -138 80 -19 -27 -37 -150 -208 -137 -27 157 62 -52 58 111
V 67 -38 -118 -17 -38 -127 -29 48 -43 36 42 -64 -87 0 -67 -25 -13 103 -80 28 -25 -93 -10 -16 62 111
E 35 -171 84 135 -201 -13 10 -175 54 -172 -82 36 -52 55 -3 13 10 -132 -191 -122 13 62 104 -33 62 111
E 15 -170 53 146 -200 -16 12 -175 78 -145 -80 43 -129 91 0 15 -19 -131 -189 -120 15 49 125 -34 62 111
V -8 38 -52 -84 1 -157 99 87 -63 20 52 -14 -163 -44 -80 -59 -12 79 -71 151 -59 -35 -69 -22 62 111
! 21
G -7 -72 -118 -133 -261 298 -153 -244 -163 -267 -185 -97 -158 -139 -180 59 -47 -157 -279 -244 58 -109 -136 -110 62 111
A 61 -121 -26 45 -138 33 78 -61 38 -116 -35 1 -134 116 -7 -4 6 -9 -150 -93 -4 -13 73 -18 62 111
E -44 -192 99 203 -219 -119 -1 -195 29 -91 -103 55 -139 104 -24 -29 -40 -152 -211 -139 -29 79 165 -49 62 111
A 149 67 -199 -140 53 -169 -59 98 -112 -3 59 -116 -177 -86 -114 -62 20 88 -69 -32 -62 -160 -119 -40 62 111
L -148 -127 -289 -248 30 -285 -111 14 -205 251 58 -218 -276 -174 -199 -204 -142 -21 -64 119 -204 -257 -219 -114 62 111
E 23 -105 -23 71 -118 -3 1 0 29 -66 -20 -6 -137 80 -15 12 46 -18 -12 -83 12 -15 75 -11 62 111
R -54 -144 -70 -8 -173 -86 -4 -23 93 -140 -63 -27 -158 33 252 -26 -45 -106 -165 -120 -26 -50 7 -46 62 111
L -114 -89 -324 -264 56 -279 -162 81 -233 207 250 -235 -263 -182 -217 -191 -57 51 -122 -104 -191 -283 -232 -109 62 111
L -167 -133 -366 -314 273 -333 -170 75 -283 192 89 -280 -304 -218 -261 -250 -158 -1 -103 -47 -250 -327 -276 -142 62 111
V -10 -72 -67 35 -58 -138 30 48 46 -27 10 -29 -146 62 -35 -15 29 96 -109 -62 -15 -49 45 -15 62 111
! 31
V -10 -95 -45 9 -107 -26 -3 -46 57 -88 -12 2 -140 60 -20 34 50 103 -130 -79 34 -23 29 -15 62 111
Y 16 -60 -103 -48 53 -154 126 -21 -32 -47 20 -9 -162 -19 -61 -54 17 -7 -68 250 -54 -59 -37 -29 62 111
P -183 -198 -230 -249 -311 -205 -240 -328 -258 -330 -291 -233 404 -254 -256 -205 -215 -283 -278 -297 -205 -231 -251 -221 62 111
E 22 -122 -25 83 -139 -125 4 -104 37 -117 -36 0 -111 111 -7 5 56 -76 271 -94 5 -13 94 -28 62 111
T 101 -52 -157 -134 -205 -83 -124 -163 -124 -195 -116 -92 -146 -107 -144 65 282 -103 -232 -197 65 -127 -124 -82 62 111
K -71 -182 -74 -7 -220 -159 0 -181 200 -57 -94 -26 -164 220 91 -62 -59 -149 -185 -140 -62 -52 81 -59 62 111
[Part of this file has been deleted for brevity]
N -78 -157 -46 -18 0 -163 124 -143 -12 -142 -79 260 -179 -9 -49 -74 -73 -121 -55 196 -74 95 -15 -56 61 111
F -195 -158 -337 -311 359 -318 -76 -15 -276 86 23 -243 -307 -214 -255 -243 -189 -52 -9 92 -243 -294 -274 -149 62 111
! 101
K -36 -165 -27 73 -196 -131 9 -164 196 -162 -76 23 -139 53 97 -26 7 -42 -180 -121 -26 -3 65 -43 62 111
L -26 -22 -189 -129 104 -172 -54 56 -44 124 65 -110 -177 -77 -1 -77 -20 95 -66 -29 -77 -153 -109 -34 62 111
L -152 -117 -372 -315 37 -333 -220 151 -287 229 88 -292 -304 -228 -269 -250 -144 93 -158 -144 -250 -335 -281 -142 62 111
S 62 -114 -37 9 -171 94 -14 -139 64 -149 -66 -10 -136 23 -14 111 19 -100 -179 -122 111 -25 15 -29 62 111
E -31 -178 80 103 -209 -28 180 -184 45 -179 -88 115 -132 103 -7 -17 8 -140 -197 -127 -17 96 103 -41 62 111
V 56 236 -210 -150 -17 -174 -63 128 -121 -1 83 -55 -181 -93 -119 -69 -20 135 -68 -32 -69 -138 -128 -45 62 111
L -45 -78 -317 -257 80 -268 -155 143 -226 187 100 -225 -258 -181 -212 -179 -95 67 -124 -100 -179 -275 -228 -101 62 111
L -71 -53 -262 -205 -32 -233 -123 171 -174 127 62 -181 -231 -19 -172 -143 -65 175 -114 -83 -143 -225 -132 -76 62 111
V -17 36 -26 -6 -67 -139 54 53 19 -52 19 -33 -147 60 -25 -36 -11 138 -101 -56 -36 -29 19 -18 62 111
V -32 73 -214 -160 -50 -175 -91 86 -134 -21 34 -134 -192 -110 -139 -55 106 220 -106 -69 -55 -177 -141 -57 62 111
! 111
L -158 -122 -373 -317 -23 -343 -232 144 -289 238 119 -299 -310 -231 -273 -261 -150 84 -167 -158 -261 -339 -283 -148 62 111
A 156 -136 -16 30 -162 -84 50 -129 85 -138 -55 3 -136 76 0 11 -21 -97 -166 -108 11 -7 48 -33 62 111
E 43 1 -1 70 -152 -120 76 -61 75 -84 -44 30 -129 52 32 36 29 -71 -158 -98 36 13 63 -19 62 111
K 16 -131 -23 32 -151 -124 240 -117 101 -127 31 16 -133 49 59 -17 10 -87 -157 -31 -17 -5 38 -31 62 111
L -47 -51 -166 -112 170 -180 222 -6 -89 77 29 -98 -185 -66 -102 -8 -40 2 -19 103 -8 -135 -94 -39 62 111
G -1 -102 -31 -9 -196 147 -43 -165 -19 -177 -95 -23 176 45 -61 31 -29 -117 -207 -153 31 -28 11 -40 62 111
K 63 -156 19 44 -187 -31 11 -160 137 -160 -70 40 -105 55 0 55 9 -119 -181 -115 55 28 48 -31 62 111
E 14 -177 158 145 -206 -118 6 -180 60 -134 -88 55 -134 49 -10 -20 -28 -117 -197 -128 -20 111 108 -42 62 111
F -50 -35 -241 -185 267 -196 -46 19 -151 34 111 -142 -199 -114 -141 -104 10 23 162 101 -104 -195 -157 -62 62 111
T -16 -105 -38 -1 -169 -16 16 -136 0 -150 -69 32 -140 7 -43 101 199 -98 -183 -128 101 -5 1 -37 62 111
! 121
P 103 50 -66 37 -142 -113 -36 -101 -14 -124 -47 -34 210 -7 -53 -23 -21 -69 -164 -116 -23 -52 20 -33 62 111
E 29 -173 83 151 -203 -117 62 -177 48 -173 -83 18 -39 129 -3 -15 -22 -122 -192 -123 -15 53 143 -39 62 111
V 55 11 -153 -95 -22 -86 4 44 -33 26 84 -86 -165 -52 -86 -50 0 155 -68 -30 -50 -122 -78 -25 62 111
Q -41 -184 56 57 -212 -120 240 -186 35 -184 -96 46 -139 218 -15 -1 -37 -145 -203 -134 -1 51 119 -54 62 111
A 186 -74 -74 -25 -107 -43 34 -67 -12 -31 -18 -36 -146 -4 -49 -2 14 -44 -136 -90 -2 -56 -17 -25 62 111
A 227 -52 -149 -115 -185 -7 -106 -146 -104 -174 -95 -84 -145 -87 -128 124 -20 1 -212 -175 124 -119 -104 -64 62 111
L -44 -27 -255 -195 159 -195 -59 33 -159 74 170 -149 -197 -120 -144 -103 -37 68 290 107 -103 -206 -166 -61 62 111
E -43 -194 155 138 -223 -118 0 -200 50 -194 -105 32 -138 157 -23 23 -24 -155 -212 -140 23 98 145 -53 62 111
K -54 -145 -64 -16 -194 -64 -19 -147 266 -161 -85 -32 -161 18 29 -54 -52 -14 -185 -138 -54 -50 -2 -55 62 111
L 79 -41 -240 -182 186 -205 -92 57 -153 105 66 -155 -208 -122 -150 -114 -48 104 -86 -49 -114 -201 -159 -58 62 111
! 131
L -26 -12 -234 -172 70 -178 -63 63 -138 105 174 -73 -182 -104 -127 -86 -20 131 -56 67 -86 -160 -146 -47 62 111
A 70 7 36 80 -183 -118 14 -155 85 -138 -66 30 -128 79 22 67 -8 -116 -177 -111 67 33 79 -30 62 111
A 53 -44 -106 -50 -46 45 -26 44 -33 11 92 -43 -156 17 -60 -16 18 50 -86 -44 -16 -77 -23 -12 62 111
V -110 -79 -337 -281 79 -291 -188 148 -253 113 56 -250 -279 -212 -241 -206 -104 236 -153 -123 -206 -296 -254 -118 62 111
A 137 139 -89 -36 -101 -54 -33 -60 -21 -86 -12 -43 -146 -11 39 74 -14 12 -132 -87 74 -68 -26 -22 62 111
T 7 -131 1 34 -151 -123 122 -42 50 -97 -44 115 -132 49 -3 32 86 -87 -158 -98 32 54 40 -23 62 111
A 128 -80 54 -15 -98 -135 -22 -38 -6 -41 -7 -32 -150 3 -45 -20 -20 100 -130 -82 -20 14 -8 -21 62 111
L -176 -137 -391 -336 -23 -364 -249 175 -305 242 113 -320 -324 -244 -287 -284 -167 37 -173 -166 -284 -358 -300 -162 62 111
A 115 -130 -19 51 -162 -62 1 -129 71 -139 -55 2 -134 41 -10 50 80 -96 -168 -109 50 -9 47 -28 62 111
A 58 -151 -15 83 -177 -123 193 -147 82 -150 41 10 -132 53 32 47 -17 -110 -174 -111 47 -3 71 -34 62 111
! 141
K 33 -166 -18 52 -199 -51 2 -168 217 -168 -81 1 -142 45 29 -9 -32 -130 -187 -127 -9 -9 49 -45 63 111
Y -201 -162 -311 -289 171 -303 -11 -103 -254 -75 63 -201 -298 -190 -234 -218 -193 -114 52 406 -218 -260 -250 -157 63 111
K -25 -137 -26 30 -91 -56 195 -45 118 -133 -49 3 -135 50 135 -20 -18 -94 -160 -102 -20 -12 37 -27 62 111
* 621 74 359 488 301 325 254 392 570 697 178 318 209 339 312 490 400 555 65 192 0 0 0 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.
-a : Use -format to set HMM output file format.
-b : Use -format to set HMM output file format.
-p : Use -format to set HMM output file format.
-P : Use -format to set HMM output file format.
-A : Set append: "N" or append: "Y" for "newhmmfile" in the ACD file
instead. Note you cannot append to an empty file or one in GCG
or Compugen (xsw) formats.
-F : Always set (an existing newhmmfile will be overwritten).
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
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
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.