ohmmindex

 

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Function

Index an HMM database

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 ohmmindex 


% ohmmindex myhmms 
Index an HMM database

Go to the output files for this example

Command line arguments 

Index an HMM database
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     HMMER hmm database file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   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 hmm database file Input file Required
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
(none)
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

ohmmindex reads any normal sequence USAs.

Output file format

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

Output files for usage example

File: myhmms

HMMER2.0
NAME  7LES_DROME/1799-1891
ACC   
DESC  
LENG  85
ALPH  Amino
RF    yes
CS    yes
MAP   yes
COM   ohmmbuild ../../data/hmm/fn3.slx -sf selex fn3.hmm
COM   ohmmcalibrate myhmms -seed 1079460101
NSEQ  109
DATE  Mon Jul 15 12:00:00 2013
CKSUM 8440
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    -7.722639   0.628102
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
          -13      *  -6769
     1  -1712  -4227  -5498   -865  -4208  -2901  -1274   -566  -2467    395  -3420  -4836   3619  -1858  -4835  -1203  -1345   -131  -4660  -1520     1
     P   -150   -501    232     46   -382    399    104   -628    211   -461   -722    274    395     44     95    358    118   -368   -296   -251 
     P   -151  -3421 -12973    -19  -6286   -701  -1378  -1013  -7392 
     2   -626  -5402   1665   -881  -5720    541  -3570  -5469  -3152   -906  -4492   -539   1858  -1555  -2021   1928   -595  -1313  -5587  -1487     3
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S     -9 -11931 -12973   -894  -1115   -701  -1378  -7406  -7384 
     3   1982  -5408  -2052    103  -5729  -1682  -3568  -5480    246  -3106  -4497  -1099   2207    785   -341    -15   -969   -591  -5592  -1728     4
     P   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     P     -9 -11931 -12973   -894  -1115   -701  -1378  -7406  -7375 
     4  -1926  -4682  -2749  -6731  -4830  -6496  -5599   -144  -6364  -1674  -3977  -6224   3833  -6035  -1363  -5637  -2263   1172  -5463  -5108     5
     P   -148   -501    232     42   -382    397    104   -620    209   -460   -713    274    394     44     98    358    116   -371   -296   -251 
     P   -133  -3608 -12999    -21  -6130   -701  -1378  -7406  -7366 
     5  -1312   -699  -1390    365   -156    656   -278  -5500    196  -1273  -1315  -1810   -383   1165   1059    988   1349  -1727   -330  -1786     7
     R   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     R    -23 -11957  -6753   -894  -1115   -701  -1378  -7406  -7358 
     6   -952  -5420   1492   -589  -2060    995   -241   -588  -1239  -1246  -4509   2702   -765    546    117  -1666  -1058  -5042  -5603  -1781     8
     N   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     N     -9 -11943 -12986   -894  -1115   -373  -2136  -7406  -7349 
     7  -1910  -4186  -1403   -683    554  -5930  -4807    398  -5685   2189    658  -5576    664  -5305  -5486  -5017  -4309   1814  -4661  -4323     9
     F   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     F    -31 -11957  -6051   -894  -1115   -701  -1378  -7406  -7340 
     8  -1843   -858  -1320   -329  -1890  -1639   2015  -1004    837  -3190  -4500   -528  -5007   1351   1283    933   1453    118  -5594  -4912    10
     S   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     S     -9 -11935 -12977   -894  -1115   -288  -2468  -7406  -7331 
     9   1390    190  -6595  -5959   1799   -625  -4670    917  -2544    -64   -175  -5444  -2246   -521  -2424  -1906  -2445   2071   -270  -4193    11
     V   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     V    -10 -11957 -12999   -894  -1115   -701  -1378  -7406  -7322 
    10  -1212   -976   -129    110  -5720  -2845   -164    383    351   -777    230  -1215  -2266   -366    198   1223   1864    -91   -385  -1640    12
     R   -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]

     V   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     V    -17 -11290 -12332   -894  -1115   -701  -1378  -7171  -6443 
    57  -2038  -3436  -5943  -5308  -1145  -5154  -4025   2255    423   1498   1203  -4797  -1707   -478  -1267  -2117  -3548   1450  -3893   -931    75
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6426 
    58    622  -4802   1764   1486  -5123  -4302  -2961  -1060    334  -4818  -3891   -420  -4396   1293   1148    487  -3268  -1087  -4985   -429    76
     D   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     D   -102 -11291  -4156   -894  -1115   -701  -1378  -7171  -6409 
    59   1265   -231  -1498   1351  -5045   -262   -355  -4796    922  -1073  -3813    778  -4318    877    -34     53    386  -2030    289  -4225    77
     Q   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     Q    -18 -11207 -12249   -894  -1115   -160  -3250  -7171  -6392 
    60   -684    813  -5723   -473    532  -2124  -3981  -2958   -121   2114   2840  -1421  -5174  -4409   -926  -4196  -1685   -376  -3915    497    78
     K   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     K    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6375 
    61  -1812  -4803   1626   -749   -515  -1133   -415  -4875  -1294  -4819  -3892   3181   -793   1470  -1377   -246  -3268  -4425  -4986   -193    79
     E   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     E    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6358 
    62  -1812  -4808  -1465     33  -1509   2998   1583  -4879    122  -4823  -3897    972  -4400  -1078  -3055  -1613   -682  -4429  -4991  -1114    80
     H   -149   -500    232     43   -378    398    105   -627    212   -466   -721    275    393     45     98    359    117   -367   -295   -250 
     H    -98  -4229 -12334    -49  -4901   -701  -1378  -7171  -6340 
    63   -676  -4701   -742  -1422    825   -589   -545    255   1702  -2571    812  -2986  -4424    796    418   -221   1302  -1179  -4912   1028    82
     R   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     R    -19 -11292 -12334   -894  -1115   -701  -1378  -7171  -6322 
    64  -3341  -4695    350   1378  -1551  -1973  -2998    477   1265     78    273  -1163     21    504  -1507  -1108    282    114    -19    473    83
     L   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     L    -19 -11292 -12334   -894  -1115   -701  -1378  -7171  -6304 
    65  -3605  -3444   -949  -2090   2356  -1177  -4010   1410  -1703   1341   -404  -1673   -747  -4487  -4679  -2139  -1048   1197  -3900    411    84
     D   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     D    -19 -11292 -12334   -894  -1115   -701  -1378  -7171  -6285 
    66   -655   -539   1179    279  -1324   1202  -2962  -1895    147   -682   1298   1427  -2056    608    756  -1119  -1893  -4419  -4982    140    85
     G   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     G    -19 -11292 -12335   -894  -1115   -701  -1378  -7171  -6267 
    67  -1814  -4814    166  -2636  -5135   2921   -568  -4885  -1333  -2415  -3903   1495  -4406   -312   -619    602  -1672  -4436  -4997  -4314    86
     R   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     R    -20 -11293 -12335   -894  -1115   -701  -1378  -7171  -6248 
    68  -3329   1217   -624   -797  -1594  -4303   1580  -4872   2069  -2414  -3890    617  -4396    283   2449   -560   -267  -2067  -4984  -1334    87
     V   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     V    -20 -11293 -12335   -894  -1115   -701  -1378  -7171  -6229 
    69    108    566  -1460    747  -1608  -4306  -2965    -30   1407  -2607  -3878    346   1033   -336    863  -1038    745    617  -4975  -4296    88
     I   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     I    -20 -11293 -12335   -894  -1115   -701  -1378  -7171  -6209 
    70  -1318  -3465   -283   -172  -3423  -2053  -3974   1957  -4721   1761   1425  -4678  -1762  -4391  -1578  -1974  -1561   1341  -3918  -3570    89
     D   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     D    -20 -11293 -12336   -894  -1115   -701  -1378  -7171  -6190 
    71  -1165  -4790   -240   -275  -5105  -4306   1035  -2009   1665   -395    707  -1334   -218   -188   1891  -1077   -383    404    110    348    90
     P   -149   -500    233     43   -381    398    106   -626    210   -464   -720    275    394     45     96    359    117   -369   -294   -249 
     P    -43  -6001 -12336   -150  -3342   -701  -1378  -7171  -6170 
    72  -1929   1218  -1535  -1647  -3990  -4677  -3410   1725    207  -1481  -3117  -3608   -810  -1118   -743  -1942    428   2687  -4324  -3869    92
     K      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     K      *      *      *      *      *      *      *  -7171      0 
//

File: myhmms.gsi

This file contains non-printing characters and so cannot be displayed here.

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
ohmmemit Extract HMM sequences
ohmmfetch Extract HMM from a 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