ehmmbuild

 

Function

Build HMM

Description

**************** EDIT HERE ****************

Algorithm

**************** EDIT HERE ****************

Usage

Here is a sample session with ehmmbuild


% ehmmbuild globins50.msf globin.hmm -auto 

hmmbuild - build a hidden Markov model from an alignment
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Training alignment:                ../../data/hmm/globins50.msf
Number of sequences:               50
Search algorithm configuration:    Local  (hmmsw)
S/W aggregate entry probability:   0.50
S/W aggregate exit probability:    0.50
Model construction strategy:       Fast/ad hoc (gapmax 0.50)
Null model used:                   (default)
Prior used:                        (default)
Prior strategy:                    Dirichlet
Sequence weighting method:         G/S/C tree weights
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Determining effective sequence number    ... done. [14]
Weighting sequences heuristically        ... done.
Constructing model architecture          ... done.
Saving count vector file                 ... done. [globins50.out3]
Converting counts to probabilities       ... done.
Setting model name, etc.                 ... done. [globins50]

Constructed a profile HMM (length 146)
Average score:      187.26 bits
Minimum score:       77.42 bits
Maximum score:      248.11 bits
Std. deviation:      47.00 bits

Finalizing model configuration           ... done.
Saving model to file                     ... done. [globin.hmm]
Saving annotated alignment               ... done. [globins50.out2]

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     Sequence set USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -priorfile          infile     Dirichlet prior file
   -nullfile           infile     NULL model file
   -pamfile            infile     PAM file
   -strategy           menu       Select preference
   -append             boolean    Append to file
   -amino              boolean    Treat as protein
   -nucleic            boolean    Treat as dna
   -archpri            float      Architecture prior
   -binary             boolean    Write HMM as binary
   -cstrategy          menu       Select strategy
   -fast               boolean    Work in fast mode
   -gapmax             float      Fast mode control
   -hand               boolean    Specify model by hand
   -idlevel            float      Cutoff ID threhold
   -[no]efficiency     boolean    Be efficient
   -pamweight          float      Weighting for PAM
   -swentry            float      Probability control for local entries
   -swexit             float      Probability control for exits
   -more               boolean    Verbosity
   -weighting          menu       Select weighting
   -resavefile         outfile    Resave selex filename
   -cfile              outfile    Emission and transition count file

   Associated qualifiers:

   "-sequences" 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
   -odirectory2        string     Output directory

   "-resavefile" associated qualifiers
   -odirectory         string     Output directory

   "-cfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-sequences]
(Parameter 1)
Sequence set USA Readable set of sequences Required
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.ehmmbuild
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-priorfile Dirichlet prior file Input file Required
-nullfile NULL model file Input file Required
-pamfile PAM file Input file Required
-strategy Select preference
M (multiple)
L (local)
G (global)
L
-append Append to file Boolean value Yes/No No
-amino Treat as protein Boolean value Yes/No No
-nucleic Treat as dna Boolean value Yes/No No
-archpri Architecture prior Any numeric value 0.85
-binary Write HMM as binary Boolean value Yes/No No
-cstrategy Select strategy
F (Fast)
H (Hand)
F
-fast Work in fast mode Boolean value Yes/No No
-gapmax Fast mode control Any numeric value 0.5
-hand Specify model by hand Boolean value Yes/No No
-idlevel Cutoff ID threhold Any numeric value 0.62
-[no]efficiency Be efficient Boolean value Yes/No Yes
-pamweight Weighting for PAM Any numeric value 20.0
-swentry Probability control for local entries Any numeric value 0.5
-swexit Probability control for exits Any numeric value 0.5
-more Verbosity Boolean value Yes/No No
-weighting Select weighting
B (Blosum)
G (Gerstein/Sonnhammer/Chothia)
K (Krogh/Mitchison)
N (None)
V (Voronoi)
G
-resavefile Resave selex filename Output file  
-cfile Emission and transition count file Output file  

Input file format

ehmmbuild reads any normal sequence USAs.

Input files for usage example

File: globins50.msf



   MSF:  171  Type: P    Check:  4694   .. 

 Name: GLB2_MORMR      oo  Len:  171  Check:  6522  Weight: 2.7687
 Name: GLBZ_CHITH      oo  Len:  171  Check:  6733  Weight: 2.9329
 Name: HBA2_BOSMU      oo  Len:  171  Check:  5006  Weight: 0.6394
 Name: HBA2_GALCR      oo  Len:  171  Check:  6652  Weight: 0.5183
 Name: HBA4_SALIR      oo  Len:  171  Check:  5434  Weight: 1.9511
 Name: HBAD_CHLME      oo  Len:  171  Check:  6621  Weight: 1.2927
 Name: HBAD_PASMO      oo  Len:  171  Check:  8118  Weight: 1.2927
 Name: HBAZ_HORSE      oo  Len:  171  Check:  8382  Weight: 1.6223
 Name: HBA_AILME       oo  Len:  171  Check:  5402  Weight: 0.4145
 Name: HBA_ANSSE       oo  Len:  171  Check:  3688  Weight: 0.8315
 Name: HBA_COLLI       oo  Len:  171  Check:  4420  Weight: 0.8557
 Name: HBA_ERIEU       oo  Len:  171  Check:  5528  Weight: 0.8390
 Name: HBA_FRAPO       oo  Len:  171  Check:  4136  Weight: 0.5014
 Name: HBA_MACFA       oo  Len:  171  Check:  5986  Weight: 0.2233
 Name: HBA_MACSI       oo  Len:  171  Check:  6064  Weight: 0.2233
 Name: HBA_MESAU       oo  Len:  171  Check:  5499  Weight: 0.6722
 Name: HBA_PAGLA       oo  Len:  171  Check:  6189  Weight: 0.5388
 Name: HBA_PHACO       oo  Len:  171  Check:  5129  Weight: 0.5014
 Name: HBA_PONPY       oo  Len:  171  Check:  5894  Weight: 0.3907
 Name: HBA_PROLO       oo  Len:  171  Check:  5810  Weight: 0.4145
 Name: HBA_TRIOC       oo  Len:  171  Check:  6427  Weight: 0.6883
 Name: HBB1_VAREX      oo  Len:  171  Check:  7239  Weight: 1.1252
 Name: HBB2_TRICR      oo  Len:  171  Check:  7790  Weight: 1.9629
 Name: HBB2_XENTR      oo  Len:  171  Check:  9537  Weight: 1.4685
 Name: HBBL_RANCA      oo  Len:  171  Check:  7490  Weight: 1.4685
 Name: HBB_CALAR       oo  Len:  171  Check:  6568  Weight: 0.4226
 Name: HBB_COLLI       oo  Len:  171  Check:  5043  Weight: 0.7672
 Name: HBB_EQUHE       oo  Len:  171  Check:  6101  Weight: 0.6734
 Name: HBB_LARRI       oo  Len:  171  Check:  5673  Weight: 0.7672
 Name: HBB_MANSP       oo  Len:  171  Check:  7148  Weight: 0.4226
 Name: HBB_ORNAN       oo  Len:  171  Check:  6249  Weight: 0.6615
 Name: HBB_RABIT       oo  Len:  171  Check:  7043  Weight: 0.5259
 Name: HBB_SPECI       oo  Len:  171  Check:  3680  Weight: 0.5422
 Name: HBB_SPETO       oo  Len:  171  Check:  4246  Weight: 0.5422
 Name: HBB_SUNMU       oo  Len:  171  Check:  5601  Weight: 0.6734
 Name: HBB_TACAC       oo  Len:  171  Check:  7133  Weight: 0.6615
 Name: HBB_TRIIN       oo  Len:  171  Check:  4009  Weight: 0.8445
 Name: HBB_TUPGL       oo  Len:  171  Check:  7197  Weight: 0.7375
 Name: HBB_URSMA       oo  Len:  171  Check:  7200  Weight: 0.4695
 Name: HBE_PONPY       oo  Len:  171  Check:  5902  Weight: 1.0101
 Name: HBF1_URECA      oo  Len:  171  Check:  6462  Weight: 2.9329
 Name: LGB1_PEA        oo  Len:  171  Check:  4791  Weight: 2.0005
 Name: LGB1_VICFA      oo  Len:  171  Check:  7426  Weight: 2.0005
 Name: MYG_ESCGI       oo  Len:  171  Check:  9170  Weight: 0.7432
 Name: MYG_HORSE       oo  Len:  171  Check:  1290  Weight: 0.7432
 Name: MYG_LYCPI       oo  Len:  171  Check:  1107  Weight: 0.8773


  [Part of this file has been deleted for brevity]

GLB2_MORMR      KLMSMICILL SSAY...... .
GLBZ_CHITH      ATFDAFFGAV FAK....... M
HBA2_BOSMU      KFLANVSTVL TSKYR..... .
HBA2_GALCR      KFMASVSTVL TSKYR..... .
HBA4_SALIR      KFLQQLALAL AEKYR..... .
HBAD_CHLME      KFLSAVAAVL AEKYR..... .
HBAD_PASMO      KFMSAVASVL AEKYR..... .
HBAZ_HORSE      KFLSIVSSVL TEKYR..... .
HBA_AILME       KFFSAVSTVL TSKYR..... .
HBA_ANSSE       KFLCAVATVL TAKYR..... .
HBA_COLLI       KFVLAVGTVL TAKYR..... .
HBA_ERIEU       KFLATVATVL TSKYR..... .
HBA_FRAPO       KFLCAVGNVL TAKYR..... .
HBA_MACFA       KFLASVSTVL TSKYR..... .
HBA_MACSI       KFLASVSTVL TSKYR..... .
HBA_MESAU       KFFASVSTVL TSKYR..... .
HBA_PAGLA       KFFSAVSTVL TSKYR..... .
HBA_PHACO       KFLCAVGTVL TAKYR..... .
HBA_PONPY       KFLASVSTVL TSKYR..... .
HBA_PROLO       KFFTSVSTVL TSKYR..... .
HBA_TRIOC       KFLCAVGNVL SAKYR..... .
HBB1_VAREX      KLVNVVSHSL ARRYH..... .
HBB2_TRICR      KLMKGVSHAL GHGY...... .
HBB2_XENTR      KLNATLVAAL SHGYF..... .
HBBL_RANCA      KFIAVLVDAL SHSYH..... .
HBB_CALAR       KVVAGVANAL AHKYH..... .
HBB_COLLI       KLVRVVAHAL ARKYH..... .
HBB_EQUHE       KVVAGVANAL AHKYH..... .
HBB_LARRI       KLVRVVAHAL ARKYH..... .
HBB_MANSP       KVVAGVANAL AHKYH..... .
HBB_ORNAN       KLVSGVAHAL GHKYH..... .
HBB_RABIT       KVVAGVANAL AHKYH..... .
HBB_SPECI       KVVAGVANAL AHKYH..... .
HBB_SPETO       KVVAGVANAL SHKYH..... .
HBB_SUNMU       KVVAGVANAL AHKYH..... .
HBB_TACAC       KLVSGVSHAL AHKYH..... .
HBB_TRIIN       KVVAGVANAL AHKYH..... .
HBB_TUPGL       KVVAGVANAL AHKYH..... .
HBB_URSMA       KVVAGVANAL AHKYH..... .
HBE_PONPY       KLVSAVAIAL AHKYH..... .
HBF1_URECA      DAAGVLVAAM .......... K
LGB1_PEA        VAYDGLATAI KKAMKT.... A
LGB1_VICFA      VAYDGLATAI K....A.... A
MYG_ESCGI       KALELFRKDI AAKYKELGFQ G
MYG_HORSE       KALELFRNDI AAKYKELGFQ G
MYG_LYCPI       KALELFRNDI AAKYKELGFQ G
MYG_MOUSE       KALELFRNDI AAKYKELGFQ G
MYG_MUSAN       GAFKIICSDI EKEYKAANFQ G
MYG_PROGU       KALELFRNDI AAKYKELGFQ G
MYG_SAISC       KALELFRNDM AAKYKELGFQ G

Output file format

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

Output files for usage example

File: globin.hmm

HMMER2.0
NAME  globins50
LENG  146
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   ehmmbuild ../../data/hmm/globins50.msf globin.hmm -auto
NSEQ  50
DATE  Fri Feb 18 10:17:03 2005
CKSUM 5854
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
          -93      *  -4000
     1  -1967  -2271  -4498  -4217  -3055   1639  -3307  -2518  -3920  -2945   2068  -3352    193  -3569  -3796    257  -2222   2801  -3514  -3205     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -1093  -8180 
     2  -1670  -1776    -76  -2279   1025  -3037   3194    232    -52   1914   -955  -2245  -3102  -1004  -2223  -2065  -1610  -1207  -2178  -1775     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8175 
     3  -1713  -1550  -3992  -3365    801  -3249  -2111  -1027  -2974    762   -736  -2876  -3301  -2606  -2796   1725   1747    269   3309  -1618     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8170 
     4   1140  -2941   1606    792  -3253  -2463  -1127   -278    -63  -2954  -2034  -1102   -473   -671  -1220    572   1661  -2558  -3131  -2454     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8165 
     5   1794  -2944    -65   -235  -3261    829  -1114   -284   1649  -2958  -2034   -134  -1104   -656  -1204     60   -589  -2564  -3130  -2449     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8160 
     6  -1748  -3220   1958   2253  -3519    172  -1355  -3271   -993   -829  -2323  -1243  -2761   1731  -1518  -1165  -1696   -335  -3410  -2713     6
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8155 
     7   -173  -2945   -205   2098  -3264  -2452  -1111   -302   1817  -2960  -2035    433  -2545   -652   -261    -62  -1417  -2566   2430  -2449     7
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8150 
     8    933  -2910  -1344   -795  -3214  -1181  -1120  -2952   2227   -837  -2004   -157  -2553   1184   -129    241    381   -316  -3104  -2432     8
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8145 
     9   1054   1483  -2717  -2142  -1752  -2967  -1753   -661   -506    965    533   1919  -3033    494  -2159    300   -763    120  -2182  -1788     9
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8140 
    10    475   -184  -3984   -927  -1458  -3217  -2087    964  -2953    185   -705  -2852     14  -2583  -2766  -2300   -535   2595   1896  -1619    10
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8134 
    11   -171  -2034  -2133  -1572  -2075  -2788  -1524   1191   1414    546  -1206    859  -2865    894  -1789    -14   -603   1034  -2415  -1962    11
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8129 


  [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 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7331 
   131   1046  -2920    936    659  -3228  -2456  -1116  -1039    363  -2931   1609   -673  -2549   2249  -1206   -311   -848    236  -3111  -2436   131
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7322 
   132   1525  -2380  -1743  -1189  -2505  -2643  -1343    -80   2077  -2311  -1534   -729  -2731    501  -1500   -603   -889   1459  -2705  -2176   132
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7313 
   133    738  -1513  -3848  -3222   -198    361  -2054    325    428   1007   -714  -2784  -3243  -2505  -2708    324  -1602   1238  -1968   1351   133
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7304 
   134    987   1437    598    -22    375   -425  -1546   -562  -1482  -1887    629    128  -2881  -1372  -1826   -262    958   1290  -2386  -1941   134
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7295 
   135   1231  -2587  -1541    216  -2769    193  -1233  -2428    -54    355  -1715   -467  -2642   -839   -418    386  -1448   1716  -2861  -2275   135
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7285 
   136    606  -2680    165    660  -2889    865  -1213  -2564    326   1588  -1802  -1227  -2627   -803  -1338  -1459   -507     11  -2936  -2329   136
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7276 
   137    804  -1523  -4031  -3398  -1482  -3248  -2124    348  -2998   1327   -725  -2891  -3297  -2625  -2804  -1588   1321   1922   1901  -1649   137
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7267 
   138   1808  -1941  -2321    901    973   -408  -1613  -1543  -1607  -1831   1197  -1869  -2928  -1483  -1921    869    632     -3  -2347  -1916   138
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7257 
   139   1340  -2950   -394    203  -3271  -2451   1896  -1633   1977  -2966  -2040   1016  -2545   -650    779    -62  -1417  -2572  -3134  -2451   139
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7248 
   140   1476  -2348  -1739    120  -2460  -2637  -1336    497    345  -2272   1946    710  -2722  -1006  -1512   -916    102  -1854  -2672   2397   140
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -14  -9069 -10111   -894  -1115   -701  -1378  -8273  -7238 
   141  -1642  -1910    588  -1926    393  -2933  -1677    165   1129   1319  -1086  -1997  -3002  -1605   1807  -1932  -1580  -1356  -2286   1485   141
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -15  -8608  -9650   -894  -1115   -701  -1378  -8273  -7229 
   142   1542   1691    488   -582  -2626   -279   -862    506   1171  -2375   -136   -872  -2282   -440    468    312  -1114  -1970  -2642  -2022   142
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8505  -9547   -894  -1115   -701  -1378  -8273  -7219 
   143   2278  -2091  -2495  -1900  -2272  -2771   3583    522  -1069  -2122  -1438  -1912  -2941  -1387    524  -1886  -1664  -1689  -2531  -2110   143
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8405  -9447   -894  -1115   -701  -1378  -8273  -7209 
   144   1313  -1624  -1590  -1030    784    176  -1023  -1263   1746    -28   1368  -1204  -2374   -799   -322   -323  -1039  -1096  -1996  -1532   144
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8405  -9447   -894  -1115   -701  -1378  -8273  -7200 
   145  -2395  -2460  -3209  -2720   1335  -3543  -1417  -2096   1716     53  -1668    854  -3574  -2202  -2474  -2599  -2321  -2018  -1148   3600   145
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -17  -8323  -9365   -894  -1115   -701  -1378  -8273  -7190 
   146  -1328  -1570  -2202  -1667   1530    183   3522  -1184  -1501  -1451   -788  -1688  -2680  -1341  -1757    347    444  -1057  -1556   1992   146
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *  -8273      0 
//

File: globins50.out2

#=AU HMMER 2.1.1
#=SQ GLB2_MORMR 0.8470 - - 0..0::0 -
#=SQ GLBZ_CHITH 0.8239 - - 0..0::0 -
#=SQ HBA2_BOSMU 0.1489 - - 0..0::0 -
#=SQ HBA2_GALCR 0.1303 - - 0..0::0 -
#=SQ HBA4_SALIR 0.7409 - - 0..0::0 -
#=SQ HBAD_CHLME 0.3489 - - 0..0::0 -
#=SQ HBAD_PASMO 0.3489 - - 0..0::0 -
#=SQ HBAZ_HORSE 0.4248 - - 0..0::0 -
#=SQ HBA_AILME  0.1053 - - 0..0::0 -
#=SQ HBA_ANSSE  0.2171 - - 0..0::0 -
#=SQ HBA_COLLI  0.2295 - - 0..0::0 -
#=SQ HBA_ERIEU  0.2144 - - 0..0::0 -
#=SQ HBA_FRAPO  0.1349 - - 0..0::0 -
#=SQ HBA_MACFA  0.0579 - - 0..0::0 -
#=SQ HBA_MACSI  0.0579 - - 0..0::0 -
#=SQ HBA_MESAU  0.1698 - - 0..0::0 -
#=SQ HBA_PAGLA  0.1330 - - 0..0::0 -
#=SQ HBA_PHACO  0.1349 - - 0..0::0 -
#=SQ HBA_PONPY  0.1013 - - 0..0::0 -
#=SQ HBA_PROLO  0.1053 - - 0..0::0 -
#=SQ HBA_TRIOC  0.1834 - - 0..0::0 -
#=SQ HBB1_VAREX 0.2835 - - 0..0::0 -
#=SQ HBB2_TRICR 0.5133 - - 0..0::0 -
#=SQ HBB2_XENTR 0.3959 - - 0..0::0 -
#=SQ HBBL_RANCA 0.3959 - - 0..0::0 -
#=SQ HBB_CALAR  0.1102 - - 0..0::0 -
#=SQ HBB_COLLI  0.1890 - - 0..0::0 -
#=SQ HBB_EQUHE  0.1760 - - 0..0::0 -
#=SQ HBB_LARRI  0.1890 - - 0..0::0 -
#=SQ HBB_MANSP  0.1102 - - 0..0::0 -
#=SQ HBB_ORNAN  0.1667 - - 0..0::0 -
#=SQ HBB_RABIT  0.1265 - - 0..0::0 -
#=SQ HBB_SPECI  0.1303 - - 0..0::0 -
#=SQ HBB_SPETO  0.1303 - - 0..0::0 -
#=SQ HBB_SUNMU  0.1699 - - 0..0::0 -
#=SQ HBB_TACAC  0.1667 - - 0..0::0 -
#=SQ HBB_TRIIN  0.1889 - - 0..0::0 -
#=SQ HBB_TUPGL  0.1889 - - 0..0::0 -
#=SQ HBB_URSMA  0.1202 - - 0..0::0 -
#=SQ HBE_PONPY  0.2359 - - 0..0::0 -
#=SQ HBF1_URECA 0.8135 - - 0..0::0 -
#=SQ LGB1_PEA   0.6773 - - 0..0::0 -
#=SQ LGB1_VICFA 0.6773 - - 0..0::0 -
#=SQ MYG_ESCGI  0.2107 - - 0..0::0 -
#=SQ MYG_HORSE  0.2107 - - 0..0::0 -
#=SQ MYG_LYCPI  0.2542 - - 0..0::0 -
#=SQ MYG_MOUSE  0.2542 - - 0..0::0 -
#=SQ MYG_MUSAN  0.8232 - - 0..0::0 -
#=SQ MYG_PROGU  0.2168 - - 0..0::0 -


  [Part of this file has been deleted for brevity]

GLB2_MORMR  ...
GLBZ_CHITH  km.
HBA2_BOSMU  ...
HBA2_GALCR  ...
HBA4_SALIR  ...
HBAD_CHLME  ...
HBAD_PASMO  ...
HBAZ_HORSE  ...
HBA_AILME   ...
HBA_ANSSE   ...
HBA_COLLI   ...
HBA_ERIEU   ...
HBA_FRAPO   ...
HBA_MACFA   ...
HBA_MACSI   ...
HBA_MESAU   ...
HBA_PAGLA   ...
HBA_PHACO   ...
HBA_PONPY   ...
HBA_PROLO   ...
HBA_TRIOC   ...
HBB1_VAREX  ...
HBB2_TRICR  ...
HBB2_XENTR  ...
HBBL_RANCA  ...
HBB_CALAR   ...
HBB_COLLI   ...
HBB_EQUHE   ...
HBB_LARRI   ...
HBB_MANSP   ...
HBB_ORNAN   ...
HBB_RABIT   ...
HBB_SPECI   ...
HBB_SPETO   ...
HBB_SUNMU   ...
HBB_TACAC   ...
HBB_TRIIN   ...
HBB_TUPGL   ...
HBB_URSMA   ...
HBE_PONPY   ...
HBF1_URECA  ...
LGB1_PEA    ...
LGB1_VICFA  ...
MYG_ESCGI   fqg
MYG_HORSE   fqg
MYG_LYCPI   fqg
MYG_MOUSE   fqg
MYG_MUSAN   ...
MYG_PROGU   fqg
MYG_SAISC   fqg

File: globins50.out3

M 0.00 0.00 0.00 0.00 0.00 3.32 0.00 0.00 0.00 0.00 1.52 0.00 0.85 0.00 0.00 1.17 0.00 7.14 0.00 0.00 
M 0.00 0.00 0.82 0.00 1.35 0.00 3.81 0.85 0.82 6.16 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.00 
M 0.00 0.00 0.00 0.00 1.06 0.00 0.00 0.00 0.00 2.30 0.00 0.00 0.00 0.00 0.00 4.23 3.29 0.85 2.28 0.00 
M 2.87 0.00 2.89 1.50 0.00 0.00 0.00 0.82 0.42 0.00 0.00 0.00 0.56 0.00 0.00 1.64 3.30 0.00 0.00 0.00 
M 4.85 0.00 0.61 0.35 0.00 2.25 0.00 0.82 3.09 0.00 0.00 0.41 0.30 0.00 0.00 0.97 0.34 0.00 0.00 0.00 
M 0.00 0.00 3.56 5.18 0.00 1.27 0.00 0.00 0.00 0.82 0.00 0.00 0.00 2.17 0.00 0.17 0.00 0.82 0.00 0.00 
M 0.82 0.00 0.51 4.83 0.00 0.00 0.00 0.81 3.56 0.00 0.00 0.82 0.00 0.00 0.42 0.85 0.00 0.00 1.36 0.00 
M 2.42 0.00 0.00 0.00 0.00 0.37 0.00 0.00 4.99 0.82 0.00 0.40 0.00 1.36 0.51 1.18 1.10 0.85 0.00 0.00 
M 2.56 0.82 0.00 0.00 0.00 0.00 0.00 0.25 0.51 2.95 0.42 3.13 0.00 0.87 0.00 1.37 0.28 0.82 0.00 0.00 
M 1.54 0.17 0.00 0.51 0.00 0.00 0.00 1.57 0.00 1.32 0.00 0.00 0.85 0.00 0.00 0.00 0.40 6.82 0.82 0.00 
M 0.82 0.00 0.00 0.00 0.00 0.00 0.00 2.23 2.69 2.21 0.00 1.35 0.00 1.16 0.00 0.99 0.35 2.18 0.00 0.00 
M 4.21 0.28 0.87 0.17 0.00 0.27 0.00 0.19 0.00 0.18 0.00 1.76 0.00 0.70 0.00 2.89 2.49 0.00 0.00 0.00 
M 2.42 0.00 0.85 0.00 0.21 0.86 0.81 2.47 0.00 0.35 0.00 0.33 0.00 0.00 0.00 2.85 0.71 2.13 0.00 0.00 
M 1.11 0.00 0.00 0.82 0.90 0.00 0.00 0.70 0.00 2.23 0.00 0.00 0.00 0.00 0.00 2.18 0.00 0.79 5.26 0.00 
M 1.26 0.00 0.34 2.00 0.81 3.77 0.00 0.00 0.00 0.51 0.00 0.00 0.00 0.68 0.00 0.82 0.32 0.00 3.47 0.00 
M 0.19 0.00 1.00 0.00 0.68 2.99 0.00 0.00 6.20 2.31 0.00 0.00 0.00 0.40 0.00 0.24 0.00 0.00 0.00 0.00 
M 0.00 0.00 0.00 0.00 0.68 0.00 0.17 2.58 4.50 1.39 0.00 1.66 0.00 0.00 0.00 0.82 0.00 2.21 0.00 0.00 
M 0.48 0.00 0.00 1.36 0.00 2.84 0.00 1.10 1.52 0.74 0.24 0.00 0.00 0.68 0.00 0.56 1.01 3.47 0.00 0.00 
M 1.95 0.00 2.09 0.00 0.00 2.54 0.13 0.85 0.81 0.00 0.42 3.27 0.74 0.68 0.00 0.27 0.25 0.00 0.00 0.00 
M 0.61 0.00 1.36 0.35 0.00 0.81 2.24 1.39 0.74 0.87 0.00 0.68 0.00 1.48 0.85 0.00 0.00 2.63 0.00 0.00 
M 3.82 0.81 1.02 1.87 0.00 1.32 0.00 1.25 0.19 0.73 0.00 0.33 1.35 0.35 0.00 0.74 0.00 0.21 0.00 0.00 
M 1.93 0.00 1.54 3.20 0.00 2.81 0.00 0.00 0.19 1.10 0.00 0.00 0.22 1.61 0.00 1.41 0.00 0.00 0.00 0.00 
M 0.66 0.38 1.57 2.78 0.00 1.15 0.00 0.41 0.00 1.67 0.00 1.50 0.00 0.81 0.00 0.22 0.00 1.13 0.85 0.87 
M 0.81 0.00 0.85 0.00 0.35 3.99 1.36 1.91 0.00 0.23 0.00 0.00 0.00 0.00 0.00 0.68 0.00 1.25 0.00 2.57 
M 1.62 0.00 0.00 0.00 0.00 7.74 0.79 1.52 0.00 0.82 0.00 0.00 0.00 0.82 0.00 0.68 0.00 0.00 0.00 0.00 
M 2.63 0.00 0.40 3.63 0.00 0.65 0.00 0.00 0.00 1.50 0.00 0.00 0.00 2.07 0.00 1.17 0.42 1.52 0.00 0.00 
M 3.00 0.51 1.37 4.05 0.68 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.00 0.74 0.82 0.19 1.11 0.00 0.00 0.85 
M 3.59 0.00 0.00 0.00 0.68 0.00 0.00 0.21 0.85 4.81 0.00 0.00 0.00 0.00 0.00 0.81 0.40 1.15 0.00 1.50 
M 1.17 0.00 0.00 0.00 0.82 2.84 0.00 0.81 0.00 5.35 0.00 0.85 0.00 0.00 0.00 0.40 1.07 0.00 0.00 0.68 
M 0.00 0.00 0.21 2.52 0.81 0.28 0.00 2.04 0.82 0.00 0.00 0.00 0.00 0.99 3.51 0.93 0.68 0.00 0.35 0.85 
M 0.00 0.00 0.00 0.85 0.81 0.25 0.00 0.68 0.00 3.99 0.00 0.00 0.00 0.82 4.88 0.22 0.00 1.50 0.00 0.00 
M 0.00 0.00 0.00 0.00 0.40 0.00 0.00 1.19 2.48 5.77 2.99 0.00 0.00 0.00 0.00 0.00 0.34 0.00 0.00 0.82 
M 0.00 0.00 0.00 0.68 4.61 0.82 0.00 0.96 0.00 1.42 0.00 0.85 0.82 0.00 0.00 0.00 0.00 3.02 0.00 0.81 
M 0.21 0.00 0.82 0.82 0.17 0.85 0.35 1.10 1.83 1.66 0.00 0.00 0.00 1.11 0.00 0.42 0.21 4.44 0.00 0.00 
M 0.89 0.00 0.00 0.00 0.00 0.85 0.00 0.00 0.68 0.00 0.00 0.77 0.00 0.00 0.00 3.26 2.32 1.76 0.00 3.47 
M 1.49 0.00 0.85 0.00 1.06 0.00 1.58 0.00 0.00 0.00 0.00 0.00 4.66 0.82 0.00 0.00 0.00 0.82 0.00 2.72 
M 0.68 0.00 0.00 0.00 0.00 0.82 0.00 0.85 0.00 0.00 0.00 0.82 6.03 0.00 0.00 0.00 0.00 0.00 3.99 0.81 
M 0.68 0.00 0.00 1.36 0.00 0.00 0.82 0.82 0.00 0.85 0.00 0.00 1.00 1.96 0.00 1.13 5.38 0.00 0.00 0.00 
M 0.68 0.00 0.00 0.00 0.82 0.81 0.00 0.00 0.68 0.82 0.00 0.00 0.00 3.47 0.51 0.00 5.35 0.85 0.00 0.00 
M 0.00 0.00 0.81 0.00 0.00 0.68 0.00 0.00 5.51 1.36 0.00 0.00 0.82 0.00 3.99 0.00 0.00 0.00 0.00 0.82 
M 2.24 0.00 0.51 0.85 3.25 0.00 0.00 0.00 0.82 1.49 0.00 0.00 0.00 0.28 0.00 0.00 3.25 0.00 0.00 1.31 
M 0.81 0.00 0.00 0.00 6.33 0.00 0.00 0.00 1.36 0.00 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.00 3.99 
M 0.19 0.00 1.26 0.76 7.67 0.00 0.51 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.00 1.94 0.85 0.00 0.00 0.00 
M 0.17 0.00 1.88 0.00 1.49 0.85 0.47 0.00 0.82 0.00 0.00 0.82 3.25 0.00 0.00 3.86 0.40 0.00 0.00 0.00 
M 0.82 0.00 0.00 0.00 4.66 0.00 4.80 0.00 2.19 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.85 0.00 0.00 0.00 
M 0.00 0.00 0.82 0.00 4.61 3.99 0.00 0.00 1.49 0.68 0.00 0.00 0.85 0.00 0.00 0.82 0.00 0.00 0.74 0.00 
M 1.59 0.00 6.62 0.00 0.81 0.00 0.00 0.00 2.04 0.82 0.00 1.29 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
M 0.85 0.00 0.68 0.00 0.00 0.82 1.11 0.00 0.00 7.06 0.00 0.25 0.00 0.00 0.00 1.55 1.50 0.17 0.00 0.00 
M 0.68 0.00 0.00 0.82 0.00 0.00 0.96 0.82 0.00 1.36 0.00 0.21 0.00 1.06 0.00 7.34 0.00 0.74 0.00 0.00 
M 2.27 0.00 0.00 0.42 0.00 0.68 1.48 0.00 1.36 0.82 0.00 0.57 0.99 1.17 0.00 3.31 0.11 0.81 0.00 0.00 


  [Part of this file has been deleted for brevity]

T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 14.00 0.00 0.00 0.00 0.00 0.00 0.00 
T 9.94 0.00 0.00 0.00 0.00 0.00 0.00 
T 9.20 0.00 0.00 0.00 0.00 0.00 0.00 
T 8.52 0.00 0.00 0.00 0.00 0.00 0.00 
T 8.52 0.00 0.00 0.00 0.00 0.00 0.00 
T 8.01 0.00 0.00 0.00 0.00 0.00 0.00 

Data files

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
ealistatStatistics for multiple alignment files
ehmmalignAlign sequences with an HMM
ehmmcalibrateCalibrate a hidden Markov model
ehmmconvertConvert between HMM formats
ehmmemitExtract HMM sequences
ehmmfetchExtract HMM from a database
ehmmindexIndex an HMM database
ehmmpfamAlign single sequence with an HMM
ehmmsearchSearch 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.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, 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.