ohmmcalibrate

 

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Function

Calibrate a hidden Markov model

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 ohmmcalibrate 


% ohmmcalibrate globin.hmm -seed 1079460101 -auto

Go to the output files for this example

Command line arguments 

Calibrate a hidden Markov model
Version: EMBOSS:6.4.0.0

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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -cpu                integer    [0] Number of CPUs (Any integer value)
   -fixed              integer    [0] Length fix for random sequences (Integer
                                  0 or more)
   -mean               float      [350.] Mean length of synthetic sequences
                                  (Any numeric value)
   -num                integer    [5000] Number of synthetic sequences (Any
                                  integer value)
   -pvm                boolean    [N] Run on parallel virtual machines
   -sd                 float      [350.] Standard deviation of syntheic
                                  sequences (Any numeric value)
   -seed               integer    [0] Random seed (Integer 0 or more)
   -histogramfile      outfile    [*.ohmmcalibrate] HMMER histogram output
                                  file (optional)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-histogramfile" 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
[-infile]
(Parameter 1)		 infile HMMER hidden markov model file Input file Required
[-outfile]
(Parameter 2)		 outfile HMMER hmmcalibrate program output file Output file <*>.ohmmcalibrate
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-cpu integer Number of CPUs Any integer value 0
-fixed integer Length fix for random sequences Integer 0 or more 0
-mean float Mean length of synthetic sequences Any numeric value 350.
-num integer Number of synthetic sequences Any integer value 5000
-pvm boolean Run on parallel virtual machines Boolean value Yes/No No
-sd float Standard deviation of syntheic sequences Any numeric value 350.
-seed integer Random seed Integer 0 or more 0
-histogramfile outfile HMMER histogram output file (optional) Output file <*>.ohmmcalibrate
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
"-histogramfile" 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

ohmmcalibrate reads any normal sequence USAs.

Output file format

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

Output files for usage example

File: globin.ohmmcalibrate

HMM file:                 ./globin.hmm
Length distribution mean: 350
Length distribution s.d.: 350
Number of samples:        5000
random seed:              1079460101
histogram(s) saved to:    globin.out2
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

HMM    : GLB2_MORMR
mu     :    -8.743577
lambda :     0.616385
max    :     2.437000
//

File: globin.out2

HMM: GLB2_MORMR
score    obs    exp  (one = represents 20 sequences)
-----    ---    ---
  -19      1      0|=                                                          
  -18      2      0|=                                                          
  -17      8      0|=                                                          
  -16      3      0|=                                                          
  -15     16      0|=                                                          
  -14    105      0|======                                                     
  -13    125      2|*======                                                    
  -12    144     87|====*===                                                   
  -11    251    481|=============           *                                  
  -10    922    978|=============================================== *          
   -9   1152   1106|=======================================================*== 
   -8    709    897|====================================        *              
   -7    701    604|==============================*=====                       
   -6    434    368|==================*===                                     
   -5    195    212|==========*                                                
   -4    115    118|=====*                                                     
   -3     61     65|===*                                                       
   -2     24     35|=*                                                         
   -1     20     19|*                                                          
    0      6     10|*                                                          
    1      4      5|*                                                          
    2      2      3|*                                                          


% Statistical details of theoretical EVD fit:
              mu =    -8.7436
          lambda =     0.6164
chi-sq statistic =    76.0060
  P(chi-square)  =  3.101e-13
//

File: globin.hmm

HMMER2.0
NAME  GLB2_MORMR
ACC   
DESC  
LENG  147
ALPH  Amino
RF    yes
CS    yes
MAP   yes
COM   ohmmbuild ../../data/hmm/globins50.msf globin.hmm -auto
COM   ohmmcalibrate globin.hmm -seed 1079460101 -auto
NSEQ  50
DATE  Fri Jul 15 12:00:00 2011
CKSUM 8939
XT      -8455     -4      0      *  -8455     -4      0      * 
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    -8.743577   0.616385
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
         -104      *  -3846
     1  -1478  -1780   -402   -384  -1798    746  -1522    195  -1557  -1660   1115  -1800    -97  -1422  -1853     13  -1419   2556  -2187  -1765     4
     P   -143   -495    230     41   -385    395    124   -625    208   -465   -725    274    391     47     92    364    113   -364   -299   -254 
     P  -1004  -1008  -9940  -2163   -365   -701  -1378  -1104  -8190 
     2  -3899  -3461  -5717   -754   -329  -5403  -3143  -1795  -4957   2999  -1134  -4739  -5080  -4188  -4625  -4609  -3788  -2395   3057  -1547    16
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L     -9  -8898  -9940   -894  -1115   -701  -1378  -8294  -8185 
     3  -1995  -2562  -4756  -4903    948  -2899  -4002  -4323  -4709  -4557  -3803  -3536  -3665  -4271  -4506   2845   2539  -3465  -4401  -3785    17
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S     -9  -8898  -9940   -894  -1115   -701  -1378  -8294  -8180 
     4   1974  -2894   1467   -816  -3309    781  -1179  -3058    963  -3017  -2101  -1116    189   -730  -1296   -776    170  -2597  -3194  -2516    18
     D   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     D     -9  -8898  -9940   -894  -1115   -701  -1378  -8294  -8175 
     5   1383  -2883    585   1876  -3204    405  -1043  -2954    287  -2899  -1973    -61  -2477    990  -1132   -921   -518   -602  -3067  -2384    19
     A   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     A     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8170 
     6  -3444  -5495   2619   2744  -5608  -3223  -2646  -5588  -3024  -5423  -4830    874  -3800   1490  -3998  -3057  -3535  -5032  -5625  -4510    20
     E   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     E     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8165 
     7  -2536  -2957  -3306  -2413  -3119  -3548  -1859    874   3060  -1039  -2114  -2413   -446  -1563    710  -2671  -2388  -2506   3242  -2796    21
     K   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     K     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8160 
     8   1087  -2878  -1251    152  -3199     57  -1039  -2949   1245  -2894  -1968   1023   -478   1653  -1127    491    694  -2500  -3062  -2379    22
     N   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     N     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8155 
     9    998   -413  -1742   -198  -2292   -825  -1300  -1037    714   1062    420   2005  -2677   -395  -1494  -1541   -425   -661  -2537  -2029    23
     K   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     K     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8150 
    10  -3221  -2748  -5841  -5461  -3140  -5557  -5075   2551  -5338  -1071  -1986  -5198  -5343  -5155  -5383  -4856  -3201   2966  -4560   1098    24
     I   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 


  [Part of this file has been deleted for brevity]

     F   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     F    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7340 
   132  -1696  -3203   2107   1686  -3513    508  -1292  -3276    -99  -3215  -2304   -545  -2698   2093  -1462    197   -974  -2821  -3384  -2676   150
     E   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     E    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7331 
   133   -206  -3207    301  -1311  -3800   -540  -1754  -3505   3357  -3525  -2667  -1586  -3037  -1345  -1850  -1908  -2007    106  -3732  -3091   151
     K   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     K    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7322 
   134   1654  -1721  -4245  -3631   2645  -3462  -2390   -910  -3244   1144   -791  -3131  -3508  -2856  -3053  -2564     87    891  -2223  -1892   152
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7313 
   135   -137  -1432  -3948  -3313   1581  -3155  -2026   -114  -2909   1428   2225   -648  -3203  -2531  -2710  -2240  -1547   1624  -1889   1109   153
     M   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     M    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7304 
   136   1325   1101   1112    721  -3197   -363  -1036  -2947    702  -1945  -1965   -289  -2471    375   -257   1183  -1037  -2498  -3059  -2377   154
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S    -13  -8968 -10010   -894  -1115   -701  -1378  -8294  -7295 
   137   1277  -1469  -3536  -2925  -1430   1509  -1928    601  -2600    216   1186  -1524  -3132   -175  -2535   -508    -85   1083  -1920  -1568   155
     M   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     M    -14  -8968 -10010   -894  -1115   -701  -1378  -8294  -7285 
   138  -3610  -3121  -6153  -5690   1786  -5837  -5020   1076  -5518   1386  -1290  -5502  -5406  -4901  -5339  -5127  -3551   2808  -4105  -3986   156
     I   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     I    -14  -8968 -10010   -894  -1115   -701  -1378  -8294  -7276 
   139   2030   2259  -3344  -2779    473   -514  -2054  -1307  -2515  -1647   -982  -2529  -3154  -2266    681   1110  -1625    881  -2225  -1864   157
     C   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     C    -14  -8968 -10011   -894  -1115   -701  -1378  -8294  -7267 
   140    502  -2761   -339   -762  -3031   -384   1988    -18   -326  -1254  -1863   1897  -2499   -629  -1172    471   1548  -2356  -2975  -2324   158
     I   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     I    -14  -8968 -10011   -894  -1115   -701  -1378  -8294  -7257 
   141   2557  -2132   1224  -2787  -2497  -3049  -2499  -1705  -2776   -586  -1671  -2638  -3386  -2536  -2949  -1127  -1982   1773  -2964  -2581   159
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L    -14  -8969 -10011   -894  -1115   -701  -1378  -8294  -7248 
   142  -4284  -3705  -6735  -6190  -2138  -6510  -5341   1840  -6011   2724   1723  -6217  -5667  -4910  -5578  -5867  -4158    115  -3948  -4121   160
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L    -14  -8884  -9926   -894  -1115   -701  -1378  -8294  -7238 
   143   1959  -2667  -1304    160    207   -440  -1064  -2658    652  -2686  -1806  -1057  -2476   -630  -1169    822   1391  -2278  -2923  -2284   161
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S    -14  -8825  -9867   -894  -1115   -701  -1378  -8294  -7229 
   144   1365  -2863  -1251   1036  -3195  -2373   3163  -2932    818  -2872  -1957  -1010  -2467   -558    298    930  -1351  -2492  -3031  -2370   162
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S    -14  -8825  -9868   -894  -1115   -701  -1378  -8294  -7219 
   145    360  -3058  -1454    144  -3448    -36  -1205  -3163   3161  -3086  -2193  -1228  -2682   -756   -274   -567  -1600  -2731  -3220  -2602   163
     A   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     A    -15  -8733  -9776   -894  -1115   -701  -1378  -8294  -7209 
   146  -5001  -4245  -5636  -5890   -650  -5388  -2113  -3919  -5374  -3258    935  -4373  -5399  -4454  -4899  -4809  -4973  -4162  -1378   4785   164
     Y   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     Y    -15  -8575  -9617   -894  -1115   -701  -1378  -8294  -7200 
   147  -3220  -3923  -3873  -2549   -201  -3790   3575  -4055   2069  -3728  -3058  -2457  -3723  -1277   2773  -3101  -2911  -3829  -3495  -3253   165
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *  -8294      0 
//

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
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.

History

Target users

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