ohmmsearch

 

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

Search sequence database with an HMM

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 ohmmsearch 


% ohmmsearch Artemia.fa ../ohmmcalibrate-ex-keep/globin.hmm -auto

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

Command line arguments 

Search sequence database with an HMM
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-hmmfile]           infile     HMMER hidden markov model file
  [-outfile]           outfile    [*.ohmmsearch] HMMER hmmsearch program
                                  output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -nalign             integer    [100] Number of alignments (Any integer
                                  value)
   -evalue             float      [10.] E-value cutoff (Any numeric value)
   -hitcut             float      [-1000000.] Hit score cutoff (Any numeric
                                  value)
   -dbsize             integer    [59021] Calc E-value for DB size n (Any
                                  integer value)
   -cpu                integer    [0] Number of CPUs (Any integer value)
   -dome               float      [1000000.] E-value domain cutoff (Any
                                  numeric value)
   -domt               float      [-1000000.] Hit score domain cutoff (Any
                                  numeric value)
   -forward            boolean    [N] Use forward algorithm
   -nulltwo            boolean    [N] Turn off second null model
   -pvm                boolean    [N] Use parallel virtual machine
   -xnu                boolean    [N] Use XNU filtering

   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        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
[-seqall]
(Parameter 1)		 seqall Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-hmmfile]
(Parameter 2)		 infile HMMER hidden markov model file Input file Required
[-outfile]
(Parameter 3)		 outfile HMMER hmmsearch program output file Output file <*>.ohmmsearch
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-nalign integer Number of alignments Any integer value 100
-evalue float E-value cutoff Any numeric value 10.
-hitcut float Hit score cutoff Any numeric value -1000000.
-dbsize integer Calc E-value for DB size n Any integer value 59021
-cpu integer Number of CPUs Any integer value 0
-dome float E-value domain cutoff Any numeric value 1000000.
-domt float Hit score domain cutoff Any numeric value -1000000.
-forward boolean Use forward algorithm Boolean value Yes/No No
-nulltwo boolean Turn off second null model Boolean value Yes/No No
-pvm boolean Use parallel virtual machine Boolean value Yes/No No
-xnu boolean Use XNU filtering Boolean value Yes/No No
Associated qualifiers
"-seqall" associated seqall qualifiers
-sbegin1
-sbegin_seqall		 integer Start of each sequence to be used Any integer value 0
-send1
-send_seqall		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_seqall		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_seqall		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_seqall		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_seqall		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_seqall		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_seqall		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_seqall		 string Input sequence format Any string  
-sdbname1
-sdbname_seqall		 string Database name Any string  
-sid1
-sid_seqall		 string Entryname Any string  
-ufo1
-ufo_seqall		 string UFO features Any string  
-fformat1
-fformat_seqall		 string Features format Any string  
-fopenfile1
-fopenfile_seqall		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory3
-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

ohmmsearch reads any normal sequence USAs.

Input files for usage example

File: Artemia.fa

>S13421 S13421 GLOBIN - BRINE SHRIMP
DKATIKRTWATVTDLPSFGRNVFLSVFAAK
PEYKNLFVEFRNIPASELASSERLLYHGGR
VLSSIDEAIAGIDTPDRAVKTLLALGERHI
SRGTVRRHFEAFSYAFIDELKQRGVESADL
AAWRRGWDNIVNVLEAGLLRRQIDLEVTGL
SCVDVANIQESWSKVSGDLKTTGSVVFQRM
INGHPEYQQLFRQFRDVDLDKLGESNSFVA
HVFRVVAAFDGIIHELDNNQFIVSTLKKLG
EQHIARGTDISHFQNFRVTLLEYLKENGMN
GAQKASWNKAFDAFEKYISMGLSSLKRVDP
ITGLSGLEKNAILSTWGKVRGNLQEVGKAT
FGKLFTAHPEYQQMFRFSQGMPLASLVESP
KFAAHTQRVVSALDQTLLALNRPSDFVYMI
KELGLDHINRGTDRSHFENYQVVFIEYLKE
TLGDSLDEFTVKSFNHVFEVIISFLNEGLR
QADIVDPVTHLTGRQKEMIKASWSKARTDL
RSLGQELFMRMFKAHPEYQTLFVNKGFADV
PLVSLREDERFISHMANVLGGFDTLLQNLD
ESSYFIYSLRNLGDAHIQRKAGTQHFRSFE
AILIPILQESQGLDAASVEAWKKFFDVSIG
VIAQGLKVATSEEADPVTGLYGKEIVALRQ
AFAAVTPRNVEIGKRVFAKLFAAHPEYKNL
FKKFEQYSVEELPSTDAFHYHISLVMNRFS
SIGKVIDDNVSFVYLLKKLGREHIKRGLSR
KQFDQFVELYIAEISSELSDTGRNGLEKVL
TFATGVIEQGLFQLGQVDSNTLTALEKQSI
QDIWSNLRSTGLQDLAVKIFTRLFSAHPEY
KLLFTGRFGNVDNINENAPFKAHLHRVLSA
FDIVISTLDDSEHLIRQLKDLGLFHTRLGM
TRSHFDNFATAFLSVAQDIAPNQLTVLGRE
SLNKGFKLMHGVIEEGLLQLERINPITGLS
AREVAVVKQTWNLVKPDLMGVGMRIFKSLF
EAFPAYQAVFPKFSDVPLDKLEDTPAVGKH
SISVTTKLDELIQTLDEPANLALLARQLGE
DHIVLRVNKPMFKSFGKVLVRLLENDLGQR
FSSFASRSWHKAYDVIVEYIEEGLQQSYKQ
DPVTGITDAEKALVQESWDLLKPDLLGLGR
KIFTKVFTKHPDYQILFTRTGFGDTPLTKL
DDNPAFGTHIIKVMRAFDHVIQILGKPKTL
MAYLRSVGADHIATNVERRHFQAFSNALIP
VMQHDLKAQLRPDAVAAWRKGLDRIIGIID
QGLIGLKEVNPQNAFSAYDIQAVQRTWALA
KPDLMGKGAMVFKQLFTDHGYQPLFSNLAQ
YEITGLEGSPELNTHARNVMAQLDTLVGSL
QNSIELGQSLAQLGKDHVPRKVNRVHFKDF
AEHFIPLMKADLGDEFTPLAESAWKRAFDV
MIATIEQGQEGSSHALSSFLTNPVA

File: ../ohmmcalibrate-ex-keep/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 
//

Output file format

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

Output files for usage example

File: s13421.ohmmsearch


Query HMM: GLB2_MORMR||
  [HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
S13421   GLOBIN - BRINE SHRIMP                           66.9    3.3e-16   1

Parsed for domains:
Sequence Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
S13421     1/1     149   284 ..     1   138 [.    66.9  3.3e-16

Alignments of top-scoring domains:
S13421: domain 1 of 1, from 149 to 284: score 66.9, E = 3.3e-16
                CS    PLSDAEKNKIRAAWDIVYKNYEKNGVDILVKFFTGTPAAQAFFPKFK
                RF    PLSDAEKNKIRAAWDIVYKNYEKNGVDILVKFFTGTPAAQAFFPKFK
                   *->vLSaeekalVkslWgKVegnaeeiGaeaLgRlFvvYPwTqryFphFg
                      +LS  + a+++  W+KV+g++   G  +++R++ ++P+ q  F +F 
      S13421   149    GLSCVDVANIQESWSKVSGDLKTTGSVVFQRMINGHPEYQQLFRQFR 195  

                CS GLTTADALKKSSDVRWHAERIINAVNDAVKSMDD   MSMKLQELSVKHA
                RF GLTTADALKKSSDVRWHAERIINAVNDAVKSMDD   MSMKLQELSVKHA
                   dLssldavkgspkvKaHGkKVltalgdavkhLDn...lkgalakLSelHa
                   d+ +ld +  s  + aH  +V++a++++++ LDn++ +  +l+kL+e H 
      S13421   196 DV-DLDKLGESNSFVAHVFRVVAAFDGIIHELDNnqfIVSTLKKLGEQH- 243  

                CS QSFYVDRQYFKVLAGII---------ADTTAPGDAGFEKLMSMI   
                RF QSFYVDRQYFKVLAGII---------ADTTAPGDAGFEKLMSMI   
                   dklrVDPeNFklLghvlvvvLaehfgkdftPevqAAwdKflagv<-*
                     ++ D  +F +++  l+ +L+e     ++ +  A+w K+++++   
      S13421   244 IARGTDISHFQNFRVTLLEYLKENG---MNGAQKASWNKAFDAF    284  


Histogram of all scores:
score    obs    exp  (one = represents 1 sequences)
-----    ---    ---
   66      1      0|=                                                          


% Statistical details of theoretical EVD fit:
              mu =    -8.7436
          lambda =     0.6164
chi-sq statistic =     0.0000
  P(chi-square)  =          0

Total sequences searched: 1

Whole sequence top hits:
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         19K

Domain top hits:
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         20K

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
ohmmindex Index an HMM database
ohmmpfam Align single sequence 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.