ehmmcalibrate

 

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Function

Calibrate HMM search statistics

Description

EMBASSY HMMER is a suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work.

Usage:
ehmmcalibrate [options] hmmfilein hmmfileout

The hmmfileout parameter is new to EMBASSY HMMER.

hmmcalibrate reads an HMM file from , scores a large number of synthesized random sequences with it, fts an extreme value distribution (EVD) to the histogram of those scores, and re-saves hmmfile now including the EVD parameters to file . hmmcalibrate may take several minutes (or longer) to run. While it is running, a temporary file called hmmfile.xxx is generated in your working directory. If you abort hmmcalibrate prematurely (ctrl-C, for instance), your original hmmfile will be untouched, and you should delete the hmmfile.xxx temporary file.

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-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-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
//

/shared/software/bin/hmmcalibrate --mean 350.000000  --num 5000  --sd 350.000000  --seed 1 ../ehmmbuild-keep/globin.hmm

Go to the input files for this example
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.

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). 

Calibrate HMM search statistics
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-inhmmfile]         infile     File containing an HMM.
  [-outhmmfile]        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 , where  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)
   -mean               float      [350.0] Set the mean length of the synthetic
                                  sequences to , where  is a positive
                                  real number. The default is 350. (Any
                                  numeric value)
   -num                integer    [5000] Set the number of synthetic sequences
                                  to , where  is a positive integer. If
                                   is less than about 1000, the ft to the
                                  EVD may fail. Higher numbers of  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)
   -pvm                boolean    [N] 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.
   -sd                 float      [350.0] Set the standard deviation of the
                                  synthetic sequence length distribution to
                                  , where  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)
   -seed               integer    [0] Set the random seed to , where  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)
   -histfile           outfile    [*.ehmmcalibrate] Save a histogram of the
                                  scores and the fitted theoretical curve to
                                  file.

   Associated qualifiers:

   "-outhmmfile" associated qualifiers
   -odirectory2        string     Output directory

   "-histfile" associated qualifiers
   -odirectory         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
[-inhmmfile]
(Parameter 1)		 infile File containing an HMM. Input file Required
[-outhmmfile]
(Parameter 2)		 outfile File containing an HMM with EVD parameters. Output file <*>.ehmmcalibrate
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-cpu integer 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 integer 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 float 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 integer 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 boolean 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 float 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 integer 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 outfile Save a histogram of the scores and the fitted theoretical curve to file. Output file <*>.ehmmcalibrate
Associated qualifiers
"-outhmmfile" associated outfile qualifiers
-odirectory2
-odirectory_outhmmfile		 string Output directory Any string  
"-histfile" associated outfile qualifiers
-odirectory string 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.

ehmmcalibrate reads any normal sequence USAs.

Input files for usage example

File: ../ehmmbuild-keep/globin.hmm

HMMER2.0  [2.3.2]
NAME  globins50
LENG  143
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /home/pmr/local/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
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 
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   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

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   /homes/user/local/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   /homes/user/local/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-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


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     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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   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 
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     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      * 
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     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
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     -   -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 
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   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 
//

Data files

None.

Notes

1. Command-line arguments

The following original HMMER options are not supported: 
-h         : Use -help to get help information instead.

The following additional options are provided: 

-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.

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.

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
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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author. Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments 

None