ohmmemit

 

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Function

Extract HMM sequences

Description

EMBASSY HMMER is a port of the original hmmer v2.2.1 applications written by 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 ohmmemit 


% ohmmemit rrm.hmm -seed 1079460101 
Extract HMM sequences
HMMER hmmemit program output file [rrm.ohmmemit]:

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Extract HMM sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     HMMER hidden markov model file
  [-outfile]           outfile    [*.ohmmemit] HMMER hmmemit program output
                                  file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -seed               integer    [0] Random seed (Integer 0 or more)
   -selex              boolean    [N] Output in selex format
   -consensus          boolean    [N] Output consensus sequence
   -number             integer    [10] Number of sequences to produce (Any
                                  integer value)

   Associated qualifiers:

   "-outfile" 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
[-infile]
(Parameter 1)		 infile HMMER hidden markov model file Input file Required
[-outfile]
(Parameter 2)		 outfile HMMER hmmemit program output file Output file <*>.ohmmemit
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-seed integer Random seed Integer 0 or more 0
-selex boolean Output in selex format Boolean value Yes/No No
-consensus boolean Output consensus sequence Boolean value Yes/No No
-number integer Number of sequences to produce Any integer value 10
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 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

ohmmemit reads any normal sequence USAs.

Input files for usage example

File: rrm.hmm

HMMER2.0
NAME  rrm
DESC  
LENG  72
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   ../src/hmmbuild -F rrm.hmm rrm.slx
COM   ../src/hmmcalibrate rrm.hmm
NSEQ  70
DATE  Wed Jul  8 08:13:25 1998
CKSUM 2768
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   -53.840649   0.214434
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      *  -6129
     1  -1234   -371  -8214  -7849  -5304  -8003  -7706   2384  -7769   2261   -681  -7660  -7694  -7521  -7816  -7346  -5543   1527  -6974  -6639     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12326   -894  -1115   -701  -1378    -21      * 
     2  -3634  -3460  -5973  -5340   3521  -2129  -4036   -831  -2054  -1257  -2663  -4822  -5229  -4557  -4735  -1979  -1569  -1476  -3893   3439     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12326   -894  -1115   -701  -1378      *      * 
     3  -5570    838  -8268  -7958  -5637  -8152  -8243   2427  -7947   -461   -539  -7805  -7843  -7878  -8124  -7550  -5559   3130  -7481  -7000     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12326   -894  -1115   -701  -1378      *      * 
     4  -1146  -4797  -1564  -2630  -1480   2769  -2963  -1850    992  -4812  -3887    737  -4397   -120    793   -205  -1019  -4418  -4981  -1059     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12326   -894  -1115   -701  -1378      *      * 
     5  -5242  -7035    445  -3538  -7284   1773  -4583  -7166  -4676  -7046  -6312   3633  -1651  -1262   -849  -1278  -5287  -6650  -7228   -291     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12326   -894  -1115   -701  -1378      *      * 
     6  -6898  -6238  -9292  -8703   -410  -9176  -7772    820  -8535   3071   -753  -8917  -8033  -7171  -7955  -8614  -6722      5  -6136  -6414     6
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    278    394     45     96    359    117   -369   -294   -249 
     -    -33  -6025 -12326   -153  -3315   -701  -1378      *      * 
     7     -5  -5297    178  -2982  -5685  -2278   -528  -5452  -1615  -5394  -4488   1396   3136  -3022  -3659    780    976  -4981  -5565  -4854     8
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -11 -11284 -12327   -894  -1115   -701  -1378      *      * 
     8  -3329  -4799   -805    543    789  -4303    572  -4868    140  -1087  -3888   -603   1691    530    183   -162    293  -2124   2317   2037     9
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -12 -11284 -12327   -894  -1115   -701  -1378      *      * 
     9   -373  -4801   2182   1353  -1426     44   -407  -1928   -366  -4817  -3891   1263  -4395  -1080   -666    295     50  -1947  -4985    397    10
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -12 -11285 -12327   -894  -1115   -701  -1378      *      * 
    10    450   1883  -5953  -5317  -1256  -1301  -4027   1322  -1847   -283   1542  -4802  -5206  -1502  -4713  -4241   2143   1615  -3893  -3551    11
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -12 -11285 -12327   -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 
     -    -17 -11290 -12332   -894  -1115   -701  -1378      *      * 
    57  -2038  -3436  -5943  -5308  -1145  -5154  -4025   2255    423   1498   1203  -4797  -1707   -478  -1267  -2117  -3548   1450  -3893   -931    75
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -18 -11291 -12333   -894  -1115   -701  -1378      *      * 
    58    622  -4802   1764   1486  -5123  -4302  -2961  -1060    334  -4818  -3891   -420  -4396   1293   1148    487  -3268  -1087  -4985   -429    76
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -   -102 -11291  -4156   -894  -1115   -701  -1378      *      * 
    59   1265   -231  -1498   1351  -5045   -262   -355  -4796    922  -1073  -3813    778  -4318    877    -34     53    386  -2030    289  -4225    77
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -18 -11207 -12249   -894  -1115   -160  -3250      *      * 
    60   -684    813  -5723   -473    532  -2124  -3981  -2958   -121   2114   2840  -1421  -5174  -4409   -926  -4196  -1685   -376  -3915    497    78
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -18 -11291 -12333   -894  -1115   -701  -1378      *      * 
    61  -1812  -4803   1626   -749   -515  -1133   -415  -4875  -1294  -4819  -3892   3181   -793   1470  -1377   -246  -3268  -4425  -4986   -193    79
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -18 -11291 -12333   -894  -1115   -701  -1378      *      * 
    62  -1812  -4808  -1465     33  -1509   2998   1583  -4879    122  -4823  -3897    972  -4400  -1078  -3055  -1613   -682  -4429  -4991  -1114    80
     -   -149   -500    232     43   -378    398    105   -627    212   -466   -721    275    393     45     98    359    117   -367   -295   -250 
     -    -98  -4229 -12334    -49  -4901   -701  -1378      *      * 
    63   -676  -4701   -742  -1422    825   -589   -545    255   1702  -2571    812  -2986  -4424    796    418   -221   1302  -1179  -4912   1028    82
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19 -11292 -12334   -894  -1115   -701  -1378      *      * 
    64  -3341  -4695    350   1378  -1551  -1973  -2998    477   1265     78    273  -1163     21    504  -1507  -1108    282    114    -19    473    83
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19 -11292 -12334   -894  -1115   -701  -1378      *      * 
    65  -3605  -3444   -949  -2090   2356  -1177  -4010   1410  -1703   1341   -404  -1673   -747  -4487  -4679  -2139  -1048   1197  -3900    411    84
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19 -11292 -12334   -894  -1115   -701  -1378      *      * 
    66   -655   -539   1179    279  -1324   1202  -2962  -1895    147   -682   1298   1427  -2056    608    756  -1119  -1893  -4419  -4982    140    85
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19 -11292 -12335   -894  -1115   -701  -1378      *      * 
    67  -1814  -4814    166  -2636  -5135   2921   -568  -4885  -1333  -2415  -3903   1495  -4406   -312   -619    602  -1672  -4436  -4997  -4314    86
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -20 -11293 -12335   -894  -1115   -701  -1378      *      * 
    68  -3329   1217   -624   -797  -1594  -4303   1580  -4872   2069  -2414  -3890    617  -4396    283   2449   -560   -267  -2067  -4984  -1334    87
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -20 -11293 -12335   -894  -1115   -701  -1378      *      * 
    69    108    566  -1460    747  -1608  -4306  -2965    -30   1407  -2607  -3878    346   1033   -336    863  -1038    745    617  -4975  -4296    88
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -20 -11293 -12335   -894  -1115   -701  -1378      *      * 
    70  -1318  -3465   -283   -172  -3423  -2053  -3974   1957  -4721   1761   1425  -4678  -1762  -4391  -1578  -1974  -1561   1341  -3918  -3570    89
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -20 -11293 -12336   -894  -1115   -701  -1378      *      * 
    71  -1165  -4790   -240   -275  -5105  -4306   1035  -2009   1665   -395    707  -1334   -218   -188   1891  -1077   -383    404    110    348    90
     -   -149   -500    233     43   -381    398    106   -626    210   -464   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -43  -6001 -12336   -150  -3342   -701  -1378      *      * 
    72  -1929   1218  -1535  -1647  -3990  -4677  -3410   1725    207  -1481  -3117  -3608   -810  -1118   -743  -1942    428   2687  -4325  -3869    92
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *      *      0 
//

Output file format

ohmmemit outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: rrm.ohmmemit

>seq1  
LFIKYLTTSCTETHLKDKFANYGEVVNIDIVLDADDGQLNGFGFIIFTSH
IEEQDAKKLDGKKYKGKVVES
>seq2  
LFVGNLHPIGRPEQLKDLFVNAYQVTQIKLLTTTTARARGYGFIEFPSHL
SVTKAVAKKSGQGLSGNPVKI
>seq3  
IYVNGLDDDVTEDELERLLREFGLFLAFQLCKQSGKFSGMAFIEYDNSDY
TQSIIRWLPGKVVMQRAITC
>seq4  
VYITNLPPGVQKQELFDVKDTYFGEHGPVVRFNISRDDDDTQTGEASGFG
FITFEQLEDDNMAINEEAFGKLIGGKKAKV
>seq5  
IFVGSVTHETTESLLKLTFSKQGGVKNINNPRDDETERSRNYATVEFTTE
EDAEAALENLRGIKINNRKLHI
>seq6  
GYVERLPEYASQKSFKNVFQKRGSIKLSKLPTIAQNRGQGFVTFSKHEQA
AAALSEMNGDELEGKKISV
>seq7  
LYVKNLPYGVDEDKIKDAFKSEGPITVKVVLIDAASLRIHGFGFIEFPSV
ADMAKAIKALEGFETFNVKIHI
>seq8  
LFVGGLTYFAKEEALYDLLSKFAQSEQISLANDPETGMSKGYAYVRYETE
EDVDKAVENLDNIIFNGRTLRR
>seq9  
IFVGNIDRKITRKEFENLFAPFGPSTVFPIIRGKNTGYAFVRYDDVQNAA
HLLESLDGTSDGAEVEKI
>seq10  
MYIGNLASDITLDDLADIFSPNVRVVSAVLLKATGHSRGFAFVEFEKEEA
ATSCIANYENTEGNGHVVPV

Data files

None.

Notes

None.

References

None.

Warnings

None.

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
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
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.

History

Target users

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

Comments 

None