ohmmalign

 

Wiki

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Function

Align sequences 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 ohmmalign 


% ohmmalign ../ohmmbuild-ex-keep/globin.hmm globins630.fa globins630.ali 
Align sequences with an HMM

Alignment saved in file globins630.ali

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

Command line arguments 

Align sequences with an HMM
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-hmmfile]           infile     HMMER hidden markov model file
  [-sequences]         seqset     (Aligned) protein sequence set filename and
                                  optional format, or reference (input USA)
  [-outfile]           outfile    [*.ohmmalign] HMMER hmmalign program output
                                  file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -mapalifile         infile     HMMER alignment file (optional)
   -withalifile        infile     HMMER heuristic alignment file (optional)
   -matchonly          boolean    [N] Only show match state alignment symbols

   Associated qualifiers:

   "-sequences" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         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
[-hmmfile]
(Parameter 1)		 infile HMMER hidden markov model file Input file Required
[-sequences]
(Parameter 2)		 seqset (Aligned) protein sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
[-outfile]
(Parameter 3)		 outfile HMMER hmmalign program output file Output file <*>.ohmmalign
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-mapalifile infile HMMER alignment file (optional) Input file Required
-withalifile infile HMMER heuristic alignment file (optional) Input file Required
-matchonly boolean Only show match state alignment symbols Boolean value Yes/No No
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin2
-sbegin_sequences		 integer Start of each sequence to be used Any integer value 0
-send2
-send_sequences		 integer End of each sequence to be used Any integer value 0
-sreverse2
-sreverse_sequences		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask2
-sask_sequences		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide2
-snucleotide_sequences		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein2
-sprotein_sequences		 boolean Sequence is protein Boolean value Yes/No N
-slower2
-slower_sequences		 boolean Make lower case Boolean value Yes/No N
-supper2
-supper_sequences		 boolean Make upper case Boolean value Yes/No N
-sformat2
-sformat_sequences		 string Input sequence format Any string  
-sdbname2
-sdbname_sequences		 string Database name Any string  
-sid2
-sid_sequences		 string Entryname Any string  
-ufo2
-ufo_sequences		 string UFO features Any string  
-fformat2
-fformat_sequences		 string Features format Any string  
-fopenfile2
-fopenfile_sequences		 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

ohmmalign reads any normal sequence USAs.

Input files for usage example

File: ../ohmmbuild-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
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 
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 
     I     -9  -8964 -10006   -894  -1115   -701  -1378  -8294  -8145 
    11      0     29  -1335   -786  -2969  -2418  -1085  -1608   1448    -65  -1823    700  -2509   1617    182    529   1205   -899  -2941  -2302    25


  [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 
//

File: globins630.fa

> BAHG_VITSP
MLDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAM
TVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDIL
DAWGKAYGVIADVfiqveadLYAQAVE
> GLB1_ANABR
PSVQGAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ
GMANDKLRGHSITLMYALQNFIDQLDNTDDLVCVVEKFAVNHITRKISAAEFGKINGPIK
KVLASKNFGDKYANAWAKLVAVVQAAL
> GLB1_ARTSX
ERVDPITGLSGLEKNAILDTWGKVRGNLQEVGKATFGKLFAAHPEYQQMFRFFQGVQLA
FLVQSPKFAAHTQRVVSALDQTLLALNRPSDQFVYMIKELGLDHINRGTDRSFVEYLKES
LGDSVDEFTVQSFGEVIVNFLNEGLRQA
> GLB1_CALSO
VSANDIKNVQDTWGKLYDQWDAVHAsKFYNKLFKDSEDISEAFVKAGTGSGIAMKRQAL
VFGAILQEFVANLNDPTALTLKIKGLCATHKTRGITNMELFAFALADLVAYMGTtISFTA
AQKASWTAVNDVILHQMSSYFATVA
> GLB1_CHITH
GPSGDQIAAAKASWNTVKNNQVDILYAVFKANPDIQTAFSQFAGKDLDSIKGTPDFSKH
AGRVVGLFSEVMDLLGNDANTPTILAKAKDFGKSHKSRASPAQLDNFRKSLVVYLKGATK
WDSAVESSWAPVLDFVFSTLKNEL
> GLB1_GLYDI
GLSAAQRQVIAATWKDIAGADNGAGVGKDCLIKFLSAHPQMAAVFGFSGASDPGVAALG
AKVLAQIGVAVSHLGDEGKMVAQMKAVGVRHKGYGNKHIKAQYFEPLGASLLSAMEHRIG
GKMNAAAKDAWAAAYADISGALISGLQS
> GLB1_LUMTE
ECLVTEGLKVKLQWASAFGHAHQRVAFGLELwkgILREHPEIKAPFSRVRGDNIYSPQF
GAHSQRVLSGLDITISMLDTPDmLAAQLAHLKVQHVERNLKPEFFDIFLKHLLHVLGDRL
GTHFDFGAWHDCVDQIIDGIKDI
> GLB1_MORMR
PIVDSGSVSPLSDAEKNKIRAAWDLVYKDYEKTGVDILVKFFTGTPAAQAFFPKFKGLT
TADDLKQSSDVRWHAERIINAVNDAVKSMDDTEKMSMKLKELSIKHAQSFYVDRQYFKVL
AGIIADTTAPGDAGFEKLMSMICILLSSAY
> GLB1_PARCH
GGTLAIQSHGDLTLAQKKIVRKTWHQLMRNKTSFVTDLFIRIFAYDPAAQNKFPQMAGM
SASQLRSSRQMQAHAIRVSSIMSEYIEELDSDILPELLATLARTHDLNKVGPAHYDLFAK
VLMEALQAELGSDFNQKTRDSWAKAFSIVQAVLLVKHG
> GLB1_PETMA
PIVDSGSVPALTAAEKATIRTAWAPVYAKYQSTGVDILIKFFTSNPAAQAFFPKFQGLT
SADQLKKSMDVRWHAERIINAVNDAVVAMDDTEKMSLKLRELSGKHAKSFQVDPQYFKVL
AAVIVDTVLPGDAGLEKLMSMICILLRSSY
> GLB1_PHESE
DCNTLKRFKVKHQWQQVFSGEhHRTEFSLHFWKEFLHDHPDLVSLFKRVQGENIYSPEF
QAHGIRVLAGLDSVIGVLDEDDTFTVQLAHLKAQHTERGTKPEYFDLFGTQLFDILGDKL
GTHFDQAAWRDCYAVIAAGIKP
> GLB1_SCAIN
PSVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ
GMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIK
KVLASKNFGDKYANAWAKLVAVVQAAL
> GLB1_TYLHE
TDCGILQRIKVKQQWAQVYSVGESRTDFAIDVFNNFFRTNPDRSLFNRVNGDNVYSPEF


  [Part of this file has been deleted for brevity]

GLSDAEWQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASE
DLKKHGNTVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKH
PGDFGADAQAAMSKALELFRNDIAAQYKELGFQG
> MYG_ROUAE
GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE
DLKKHGATVLTALGGILKKKGQHEAQLKPLAQSHATKHKIPVKYLEFISEVIIQVLQSKH
PGDFGADAQGAMGKALELFRNDIAAKYKELGFQG
> MYG_SAISC
GLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASE
ELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKH
PGDFGADAQGAMKKALELFRNDMAAKYKELGFQG
> MYG_SHEEP
GLSDGEWQLVLNAWGKVEADVAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASE
DLKKHGNTVLTALGGILKKKGHHEAEVKHLAESHANKHKIPVKYLEFISDAIIHVLHAKH
PSNFGADAQGAMSKALELFRNDMAAEYKVLGFQG
> MYG_SPAEH
GLSDGEWQLVLNVWGKVEGDLAGHGQEVLIKLFKNHPETLEKFDKFKHLKSEDEMKGSE
DLKKHGNTVLTALGGILKKKGQHAAEIQPLAQSHATKHKIPIKYLEFISEAIIQVLQSKH
PGDFGADAQGAMSKALELFRNDIAAKYKELGFQG
> MYG_TACAC
GLSDGEWQLVLKVWGKVETDITGHGQDVLIRLFKTHPETLEKFDKFKHLKTEDEMKASA
DLKKHGGVVLTALGSILKKKGQHEAELKPLAQSHATKHKISIKFLEFISEAIIHVLQSKH
SADFGADAQAAMGKALELFRNDMATKYKEFGFQG
> MYG_THUAL
ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAH
GATVLKKLGELLKAKGSHAAILKPLANSHATKHKIPINNFKLISEVLVKVMHEKAGLDAG
GQTALRNVMGIIIADLEANYKELGFSG
> MYG_TUPGL
GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKTEDEMKASE
DLKKHGNTVLSALGGILKKKGQHEAEIKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKH
PGDFGADAQAAMSKALELFRNDIAAKYKELGFQG
> MYG_TURTR
GLSDGEWQLVLNVWGKVEADLAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEADMKASE
DLKKHGNTVLTALGAILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PAEFGADAQGAMNKALELFRKDIAAKYKELGFHG
> MYG_VARVA
GLSDEEWKKVVDIWGKVEPDLPSHGQEVIIRMFQNHPETQDRFAKFKNLKTLDEMKNSE
DLKKHGTTVLTALGRILKQKGHHEAEIAPLAQTHANTHKIPIKYLEFICEVIVGVIAEKH
SADFGADSQEAMRKALELFRNDMASRYKELGFQG
> MYG_VULCH
GLSDGEWQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSE
DLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKH
SGDFHADTEAAMKKALELFRNDIAAKYKELGFQG
> MYG_ZALCA
GLSDGEWQLVLNIWGKVEADLVGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKRSE
DLKKHGKTVLTALGGILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLQSKH
PGDFGADTHAAMKKALELFRNDIAAKYRELGFQG
> MYG_ZIPCA
GLSEAEWQLVLHVWAKVEADLSGHGQEILIRLFKGHPETLEKFDKFKHLKSEAEMKASE
DLKKHGHTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRH
PSDFGADAQAAMTKALELFRKDIAAKYKELGFHG

Output file format

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

Output files for usage example

File: globins630.ali

#=AU HMMER 2.1.1
#=SQ BAHG_VITSP 1.0000 BAHG_VITSP - 0..0::0 -
#=SQ GLB1_ANABR 1.0000 GLB1_ANABR - 0..0::0 -
#=SQ GLB1_ARTSX 1.0000 GLB1_ARTSX - 0..0::0 -
#=SQ GLB1_CALSO 1.0000 GLB1_CALSO - 0..0::0 -
#=SQ GLB1_CHITH 1.0000 GLB1_CHITH - 0..0::0 -
#=SQ GLB1_GLYDI 1.0000 GLB1_GLYDI - 0..0::0 -
#=SQ GLB1_LUMTE 1.0000 GLB1_LUMTE - 0..0::0 -
#=SQ GLB1_MORMR 1.0000 GLB1_MORMR - 0..0::0 -
#=SQ GLB1_PARCH 1.0000 GLB1_PARCH - 0..0::0 -
#=SQ GLB1_PETMA 1.0000 GLB1_PETMA - 0..0::0 -
#=SQ GLB1_PHESE 1.0000 GLB1_PHESE - 0..0::0 -
#=SQ GLB1_SCAIN 1.0000 GLB1_SCAIN - 0..0::0 -
#=SQ GLB1_TYLHE 1.0000 GLB1_TYLHE - 0..0::0 -
#=SQ GLB2_ANATR 1.0000 GLB2_ANATR - 0..0::0 -
#=SQ GLB2_CALSO 1.0000 GLB2_CALSO - 0..0::0 -
#=SQ GLB2_CHITH 1.0000 GLB2_CHITH - 0..0::0 -
#=SQ GLB2_LUMTE 1.0000 GLB2_LUMTE - 0..0::0 -
#=SQ GLB2_MORMR 1.0000 GLB2_MORMR - 0..0::0 -
#=SQ GLB2_TYLHE 1.0000 GLB2_TYLHE - 0..0::0 -
#=SQ GLB3_CHITH 1.0000 GLB3_CHITH - 0..0::0 -
#=SQ GLB3_CHITP 1.0000 GLB3_CHITP - 0..0::0 -
#=SQ GLB3_LAMSP 1.0000 GLB3_LAMSP - 0..0::0 -
#=SQ GLB3_MORMR 1.0000 GLB3_MORMR - 0..0::0 -
#=SQ GLB3_MYXGL 1.0000 GLB3_MYXGL - 0..0::0 -
#=SQ GLB3_PETMA 1.0000 GLB3_PETMA - 0..0::0 -
#=SQ GLB3_TYLHE 1.0000 GLB3_TYLHE - 0..0::0 -
#=SQ GLB4_CHITH 1.0000 GLB4_CHITH - 0..0::0 -
#=SQ GLB4_GLYDI 1.0000 GLB4_GLYDI - 0..0::0 -
#=SQ GLB4_LUMTE 1.0000 GLB4_LUMTE - 0..0::0 -
#=SQ GLB4_TYLHE 1.0000 GLB4_TYLHE - 0..0::0 -
#=SQ GLB5_PETMA 1.0000 GLB5_PETMA - 0..0::0 -
#=SQ GLB6_CHITH 1.0000 GLB6_CHITH - 0..0::0 -
#=SQ GLB7_ARTSX 1.0000 GLB7_ARTSX - 0..0::0 -
#=SQ GLB7_CHITH 1.0000 GLB7_CHITH - 0..0::0 -
#=SQ GLB8_CHITH 1.0000 GLB8_CHITH - 0..0::0 -
#=SQ GLB9_CHITH 1.0000 GLB9_CHITH - 0..0::0 -
#=SQ GLBA_ANATR 1.0000 GLBA_ANATR - 0..0::0 -
#=SQ GLBA_SCAIN 1.0000 GLBA_SCAIN - 0..0::0 -
#=SQ GLBB_ANATR 1.0000 GLBB_ANATR - 0..0::0 -
#=SQ GLBB_SCAIN 1.0000 GLBB_SCAIN - 0..0::0 -
#=SQ GLBC_CAUAR 1.0000 GLBC_CAUAR - 0..0::0 -
#=SQ GLBC_CHITH 1.0000 GLBC_CHITH - 0..0::0 -
#=SQ GLBD_CAUAR 1.0000 GLBD_CAUAR - 0..0::0 -
#=SQ GLBD_CHITH 1.0000 GLBD_CHITH - 0..0::0 -
#=SQ GLBE_CHITH 1.0000 GLBE_CHITH - 0..0::0 -
#=SQ GLBF_CHITH 1.0000 GLBF_CHITH - 0..0::0 -
#=SQ GLBH_CHITH 1.0000 GLBH_CHITH - 0..0::0 -
#=SQ GLBI_CHITP 1.0000 GLBI_CHITP - 0..0::0 -
#=SQ GLBM_ANATR 1.0000 GLBM_ANATR - 0..0::0 -


  [Part of this file has been deleted for brevity]

MYG_GALJA   ................................................
MYG_GLOME   ................................................
MYG_GORBE   ................................................
MYG_GRAGE   ................................................
MYG_HALGR   ................................................
MYG_HETPO   ................................................
MYG_HORSE   ................................................
MYG_HUMAN   ................................................
MYG_HYLAG   ................................................
MYG_INIGE   ................................................
MYG_KOGSI   ................................................
MYG_LAGLA   ................................................
MYG_LAGMA   ................................................
MYG_LEPMU   ................................................
MYG_LOXAF   ................................................
MYG_LUTLU   ................................................
MYG_LYCPI   ................................................
MYG_MACFA   ................................................
MYG_MACRU   ................................................
MYG_MEGNO   ................................................
MYG_MELME   ................................................
MYG_MESCA   ................................................
MYG_MOUSE   ................................................
MYG_MUSAN   ................................................
MYG_NYCCO   ................................................
MYG_OCHPR   ................................................
MYG_ORCOR   ................................................
MYG_ORNAN   ................................................
MYG_ORYAF   ................................................
MYG_PANTR   ................................................
MYG_PAPAN   ................................................
MYG_PERPO   ................................................
MYG_PHOPH   ................................................
MYG_PHYCA   ................................................
MYG_PIG     ................................................
MYG_PONPY   ................................................
MYG_PROGU   ................................................
MYG_RABIT   ................................................
MYG_ROUAE   ................................................
MYG_SAISC   ................................................
MYG_SHEEP   ................................................
MYG_SPAEH   ................................................
MYG_TACAC   ................................................
MYG_THUAL   ................................................
MYG_TUPGL   ................................................
MYG_TURTR   ................................................
MYG_VARVA   ................................................
MYG_VULCH   ................................................
MYG_ZALCA   ................................................
MYG_ZIPCA   ................................................

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
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.

History

Target users

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