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EMBOSS: ehmmfetch
ehmmfetch

 

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

Retrieve an HMM from an HMM database

Description

EMBASSY HMMER is a suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work.

Usage:
ehmmfetch [options] database name outfile

The outfile parameter is new to EMBASSY HMMER.

hmmfetch is a small utility that retrieves an HMM called of a given name from a HMMER model database , in a new format, and prints that model to file . For example, 'hmmfetch Pfam rrm my.file' retrieves the RRM (RNA recognition motif) model from Pfam, if the environment variable HMMERDB is set to the location of the Pfam database. The retrieved HMM file is written in HMMER 2 ASCII format. The database must have an associated GSI index file. To index an HMM database, use the program hmmindex.

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 ehmmfetch 


% ehmmfetch ../ehmmindex-ex-keep/myhmmso pkinase pkinase.ehmmfetch 
Retrieve an HMM from an HMM database.


/shared/software/bin/hmmfetch ../ehmmindex-ex-keep/myhmmso pkinase > pkinase.ehmmfetch

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

Command line arguments

Where possible, the same command-line qualifier names and parameter order is used as in the original hmmer. There are however several unavoidable differences and these are clearly documented in the "Notes" section below.

More or less all options documented as "expert" in the original hmmer user guide are given in ACD as "advanced" options (-options must be specified on the command-line in order to be prompted for a value for them). 

Retrieve an HMM from an HMM database.
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-database]          infile     HMMER hmm database file
  [-name]              string     Entry name (Any string)
  [-outfile]           outfile    [*.ehmmfetch] HMMER hidden markov model
                                  output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -nhmm               boolean    Interpret name as an HMM number instead of a
                                  name. Numbering starts at 0. For example,
                                  to fetch the frst HMM from an HMM database
                                  called foo, you would do 'hmmfetch -n 0
                                  foo'.

   Associated qualifiers:

   "-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
[-database]
(Parameter 1)		 infile HMMER hmm database file Input file Required
[-name]
(Parameter 2)		 string Entry name Any string  
[-outfile]
(Parameter 3)		 outfile HMMER hidden markov model output file Output file <*>.ehmmfetch
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-nhmm boolean Interpret name as an HMM number instead of a name. Numbering starts at 0. For example, to fetch the frst HMM from an HMM database called foo, you would do 'hmmfetch -n 0 foo'. Boolean value Yes/No No
Associated qualifiers
"-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

Alignment and sequence formats

Input and output of alignments and sequences is limited to the formats that the original hmmer supports. These include stockholm, SELEX, MSF, Clustal, Phylip and A2M /aligned FASTA (alignments) and FASTA, GENBANK, EMBL, GCG, PIR (sequences). It would be fairly straightforward to adapt the code to support all EMBOSS-supported formats.

Compressed input files

Automatic processing of gzipped files is not supported.

ehmmfetch reads any normal sequence USAs.

Input files for usage example

File: ../ehmmindex-ex-keep/myhmmso

HMMER2.0  [2.3.2]
NAME  rrm
LENG  77
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /shared/software/bin/hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/rrm.sto
COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ  90
DATE  Thu Jul 15 12:00:00 2010
CKSUM 8325
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   -45.860321   0.213107
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
          -16      *  -6492
     1  -1084    390  -8597  -8255  -5793  -8424  -8268   2395  -8202   2081  -1197  -8080  -8115  -8020  -8297  -7789  -5911   1827  -7525  -7140     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378    -16      * 
     2  -2140  -3785  -6293  -2251   3226  -2495   -727   -638  -2421   -545   -675  -5146  -5554  -4879  -1183  -2536  -1928    267     76   3171     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     3  -2542    458  -8584  -8273  -6055  -8452  -8531   2304  -8255   -324    101  -8104  -8170  -8221  -8440  -7840  -5878   3145  -7857  -7333     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     4  -1505  -5144  -1922   -558  -1842   2472  -3303  -2213   1099  -5160  -4233    372  -4738   -530   1147    168    498  -4766  -5327  -1476     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     5  -3724  -5184    300  -3013  -1655   1803  -3353  -5245  -1569  -2686  -4276   3495  -1963  -1331  -1054  -1472  -3664  -4803  -5369     -2     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     6  -1569  -6106  -8967  -8363    555  -8531  -7279    654  -8092   2953    -94  -8220  -7908  -1643  -7682  -7771  -6460    -59  -6191  -6284     6
     -   -151   -504    230     45   -380    399    101   -621    211   -470   -713    278    399     48     91    360    113   -364   -299   -254 
     -   -178  -3113 -12684  -1600   -578   -701  -1378      *      * 
     7   -409  -5130   -215  -2987  -1709   -956    690  -5188   -395  -5144  -4224    729   3054  -2862  -3409    354   1293  -1381  -5321  -4644    13
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     8  -3674  -5118  -1004    639    420  -4652    176  -2050    404  -1039   -935     16   1755    168    147   -275    198  -1472   1889   1977    14
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
     9   -408  -5134   2415   1299   -950    -66   -767  -1296  -2889  -1843  -4224   1084   -968  -1439  -1854    540   -314  -2304  -5320    -60    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
    10    586   1804  -6294   -631  -1627  -1671  -4374   1029  -2223   -162   1172  -5147  -5554  -1870  -5058  -2327   1741   1687  -4242    687    16
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      * 
    11  -2134  -5144    845  -1187  -1652  -1667  -3303  -5216   -513   -801  -4233   1026  -1873   -543   -619    575   2956  -4766  -5327  -4644    17


  [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 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   279  -7207  -7306  -8076  -6588  -8459  -7223  -5448  -7982  -1500  -7531  -6953  -6369  -7277  -5081   4236  -7139  -6862  -7777  -7053  -7277   454
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   280   -694   -163  -5922  -5286  -1204  -2048   -610   1082  -1800   1434  -2618  -4776   2951  -4509  -4688  -1216  -1648  -2829    202     21   455
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -  -3168 -11253   -171   -894  -1115   -701  -1378      *      * 
   281  -1412  -2132  -2007  -2293  -4366   3113  -2847  -4225  -3107  -4377  -3503   1660  -2881  -2661  -3396    961  -1821  -3134  -4516  -4119   456
     -   -150   -489    232     42   -382    400    104   -627    211   -465   -722    274    393     51     95    359    116   -370   -296   -245 
     -  -2121   -637  -2975   -831  -1191  -6099    -21      *      * 
   282   -968  -1818  -1787  -1351  -3112    953  -1494  -2818  -1122  -2911  -2044  -1365  -2340  -1133   1510   1816   2121  -2205  -3137  -2649   459
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -   -228  -7899  -2816   -894  -1115  -4964    -47      *      * 
   283    840  -1663   -994    969   1159    503   -604  -1413   -325  -1594   -814   -688  -1996   -267   1103   -851   -755  -1179   2900  -1437   460
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -7938  -8980   -894  -1115    -89  -4060      *      * 
   284  -3257  -4642   -697  -2590  -1218   -252  -2907  -4655  -1306  -2353   -529    482  -1607  -2459  -1398   2112   2745  -4246  -4848  -4187   461
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11183 -12226   -894  -1115   -186  -3045      *      * 
   285   2163    763  -1619  -5296   2250  -2060  -4007   1241  -4891   -489    484  -4781   -226  -4515  -4692   -678  -1688   -813    264  -3530   462
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   286   -268   -329   -158    917   -541  -1990    350  -4851   1273  -1075    388  -1130    233    840    993   -602    801   -595  -4964   -857   463
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   287    109   -243    672   2304  -5103  -4283    488  -4854  -1317  -2269   -656   -492  -1519   2679   -655   -618  -3248  -4404  -4965  -1114   464
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   288   1312   1294  -6215  -5593   -206  -1244  -4339   2188  -5201   1409    395  -5091  -5478  -4828  -5009  -4538  -3794   1162  -4187  -3846   465
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -23 -11253  -6022   -894  -1115   -701  -1378      *      * 
   289  -3562    799  -5767  -2054  -1235  -2075    318    138    237   2164   1713  -1454  -5145  -1272   -730  -4172  -1640   1071  -3865    -34   466
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11231 -12273   -894  -1115  -1470   -646      *      * 
   290     73   1351   -674   1236  -1549  -2008   1350  -4834   1049  -2498  -3851   1801  -4356   1813   -115   -223  -1582  -1052  -4945  -4262   467
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      * 
   291  -1739   -320    777  -2654  -1419  -2051   4360  -4707  -1358  -2412   -689  -1300  -4399   -224    537    531   -289  -2010  -4905  -1057   468
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
   292  -3345  -4494   -233   -332   -563  -1986  -3051    333     99   1063  -3616  -3072   2953  -1026  -1490   -943  -1528  -1070  -4753  -4151   469
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -10815 -11857   -894  -1115   -701  -1378      *      * 
   293  -6409  -5751  -7614  -7636   2593  -7311  -4003  -5084  -7219   -150   -151  -6210  -7172   -849  -6723  -6510  -6299  -1387   4881   2807   470
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -10749 -11791   -894  -1115   -701  -1378      *      * 
   294  -4057  -3817  -6415  -5791   3203  -1638  -4541   1679  -5412    765   1434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *      *      0 
//

Output file format

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

Output files for usage example

File: pkinase.ehmmfetch

HMMER2.0  [2.3.2]
NAME  pkinase
ACC   PF00069
DESC  Protein kinase domain
LENG  294
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /shared/software/bin/hmmbuild -n pkinase --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/pkinase.sto
COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ  67
DATE  Thu Jul 15 12:00:00 2010
CKSUM 4536
GA    -57.9 -57.9
TC    -57.7 -57.7
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   -193.864685   0.143557
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      *  -6109
     1  -3588  -3415  -5932  -2068   2209  -1198  -4007   1029  -4891    889  -2618  -4781  -5186  -4515  -1612  -2029  -1657   -333   1774   3270     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378    -21      * 
     2  -1103   -137  -1497   1525  -5095  -4284   1704    -69    423  -1097  -3867   -503  -4377   1172   1017  -1013    975    769  -4962  -4280     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     3  -3460   -131   -785   -393   1050  -4703  -3447   1378    306   1185   -596   -562  -1734   -284    173  -1848     58    960  -4250  -1088     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     4  -3367  -4343   -251    -58  -1421   1411    919    542    574    989   -604    -23  -4523   -994  -3271  -1049  -1512    847  -4637   -148     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     5  -1098  -4782   -183   1680  -5103    503   -434  -4854   1124  -4798   -647  -1288  -1568   1359   1836   -240  -1526  -1059     97  -4283     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     6  -1811   -238   -680    526   -557  -4309    481    726   1770   -409  -3794  -2960    209    272    290  -1047    576    765  -4901  -4244     6
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     7  -6084  -5527  -8663  -8230  -4683  -8506  -7801   2582  -2005   2411   -444  -8189  -7866  -7357  -7914  -7892  -6017    898  -6516  -6551     7
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     8  -1162  -4907  -7014  -7376  -7618   3734  -6813  -7450  -7402  -7698  -6730  -5890  -5975   -453  -7118  -4539  -1742  -6121  -7823  -7778     8
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      * 
     9     21  -4782  -1460   1735  -1488  -2091  -2941  -1034    378  -4798   -702   -451  -1594   1320   1488   1403   -804  -2034  -4965  -4282     9
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     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *      *      0 
//

Data files

None.

Notes

1. Command-line arguments

The following original HMMER options are not supported: 
-h         : Use -help to get help information instead.
-n         : Use -nhmm instead (-n causes problems for GUI developers)

The following additional options are provided: 

-outfile   : Output file with HMM.

2. Installing EMBASSY HMMER

The EMBASSY HMMER package contains "wrapper" applications providing an EMBOSS-style interface to the applications in the original HMMER package version 2.3.2 developed by Sean Eddy. Please read the file INSTALL in the EMBASSY HMMER package distribution for installation instructions.

3. Installing original HMMER

To use EMBASSY HMMER, you will first need to download and install the original HMMER package. Please read the file 00README in the the original HMMER package distribution for installation instructions: 
WWW home:       http://hmmer.wustl.edu/
Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/

4. Setting up HMMER

For the EMBASSY HMMER package to work, the directory containing the original HMMER executables *must* be in your path. For example if you executables were installed to "/usr/local/hmmer/bin", then type: 
set path=(/usr/local/hmmer/bin/ $path)
rehash

5. Getting help

Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory. The first 3 chapters (Introduction, Installation and Tutorial) are particularly useful.

Please read the 'Notes' section below for a description of the differences between the original and EMBASSY HMMER, particularly which application command line options are supported.

References

None.

Warnings

Types of input data

hmmer v3.2.1 and therefore EMBASSY HMMER is only recommended for use with protein sequences. If you provide a non-protein sequence you will be reprompted for a protein sequence. To accept nucleic acid sequences you must replace instances of < type: "protein" > in the application ACD files with .

Environment variables

The original hmmer uses BLAST environment variables (below), if defined, to locate files. The EMBASSY HMMER does not. 
BLASTDB   location of sequence databases to be searched
BLASMAT   location of substitution matrices
HMMERDB   location of HMMs

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
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
oalistat Statistics for multiple alignment files
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
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. Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

This program is an EMBASSY wrapper to a program written by Sean Eddy as part of his hmmer package.

Please report any bugs to the EMBOSS bug team in the first instance, not to Sean Eddy.

History

Target users

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