| ehmmalign

## 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

Align sequences to an HMM profile

## 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:
ehmmalign [options] hmmfile seqfile outfile

The outfile parameter is new to EMBASSY HMMER. The multiple sequence alignment is always written to outfile. The name of outfile is specified by the -o option as normal.

hmmalign reads an HMM profile and a set of sequences , aligns the sequences to the profile HMM, and outputs a multiple sequence alignment . The set of sequences may be unaligned or aligned. If it is aligned, the existing alignment is ignored and hmmalign will align them the way it wants.

## 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 ehmmalign

    % ehmmalign ../ehmmcalibrate-ex-keep/globino.hmm globins630.fa globins630.ali
    Align sequences to an HMM profile

    hmmalign - align sequences to an HMM profile
    HMMER 2.3.2 (Oct 2003)
    Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
    Freely distributed under the GNU General Public License (GPL)
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    HMM file:             ../ehmmcalibrate-ex-keep/globino.hmm
    Sequence file:        ./ehmmalign-1234567890.1234
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

    Alignment saved in file globins630.ali

    /shared/software/bin/hmmalign  --informat FASTA --outformat A2M  -o globins630.ali ../ehmmcalibrate-ex-keep/globino.hmm ./ehmmalign-1234567890.1234

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).

    Align sequences to an HMM profile
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers:
      [-hmmfile]           infile     File containing a HMM profile
      [-seqfile]           seqset     File containing a (set of) sequence(s)
      [-o]                 align      [*.ehmmalign] Multiple sequence alignment
                                      output file.

       Additional (Optional) qualifiers:
       -m                  boolean    [N] Include in the alignment only those
                                      symbols aligned to match states. Do not show
                                      symbols assigned to insert states.
       -q                  boolean    [N] Quiet; suppress all output except the
                                      alignment itself. Useful for piping or
                                      redirecting the output.

       Advanced (Unprompted) qualifiers:
       -mapali             infile     Reads an alignment from file and aligns it
                                      as a single object to the HMM; e.g. the
                                      alignment in file is held fixed. This allows
                                      you to align sequences to a model with
                                      hmmalign and view them in the context of an
                                      existing trusted multiple alignment. The
                                      alignment to the alignment is defined by a
                                      'map' kept in the HMM, and so is fast and
                                      guaranteed to be consistent with the way the
                                      HMM was constructed from the alignment. The
                                      alignment in the file must be exactly the
                                      alignment that the HMM was built from.
                                      Compare the -withali option.
       -withali            infile     Reads an alignment from file and aligns it
                                      as a single object to the HMM; e.g. the
                                      alignment in file is held fixed. This allows
                                      you to align sequences to a model with
                                      hmmalign and view them in the context of an
                                      existing trusted multiple alignment. The
                                      alignment to the alignment is done with a
                                      heuristic (nonoptimal) dynamic programming
                                      procedure, which may be somewhat slow and is
                                      not guaranteed to be completely consistent
                                      with the way the HMM was constructed (though
                                      it should be quite close). However, any
                                      alignment can be used, not just the
                                      alignment that the HMM was built from.
                                      Compare the -mapali option.

       Associated qualifiers:

       "-seqfile" 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

       "-o" associated qualifiers
       -aformat3           string     Alignment format
       -aextension3        string     File name extension
       -adirectory3        string     Output directory
       -aname3             string     Base file name
       -awidth3            integer    Alignment width
       -aaccshow3          boolean    Show accession number in the header
       -adesshow3          boolean    Show description in the header
       -ausashow3          boolean    Show the full USA in the alignment
       -aglobal3           boolean    Show the full sequence in alignment

       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 | File containing a HMM profile | Input file | Required
[-seqfile] (Parameter 2) | seqset | File containing a (set of) sequence(s) | Readable set of sequences | Required
[-o] (Parameter 3) | align | Multiple sequence alignment output file. | Alignment output file | <*>.ehmmalign
Additional (Optional) qualifiers
-m | boolean | Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. | Boolean value Yes/No | No
-q | boolean | Quiet; suppress all output except the alignment itself. Useful for piping or redirecting the output. | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers
-mapali | infile | Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a 'map' kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file must be exactly the alignment that the HMM was built from. Compare the -withali option. | Input file | Required
-withali | infile | Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. Compare the -mapali option. | Input file | Required
Associated qualifiers
"-seqfile" associated seqset qualifiers
-sbegin2 -sbegin_seqfile | integer | Start of each sequence to be used | Any integer value | 0
-send2 -send_seqfile | integer | End of each sequence to be used | Any integer value | 0
-sreverse2 -sreverse_seqfile | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask2 -sask_seqfile | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide2 -snucleotide_seqfile | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein2 -sprotein_seqfile | boolean | Sequence is protein | Boolean value Yes/No | N
-slower2 -slower_seqfile | boolean | Make lower case | Boolean value Yes/No | N
-supper2 -supper_seqfile | boolean | Make upper case | Boolean value Yes/No | N
-sformat2 -sformat_seqfile | string | Input sequence format | Any string |
-sdbname2 -sdbname_seqfile | string | Database name | Any string |
-sid2 -sid_seqfile | string | Entryname | Any string |
-ufo2 -ufo_seqfile | string | UFO features | Any string |
-fformat2 -fformat_seqfile | string | Features format | Any string |
-fopenfile2 -fopenfile_seqfile | string | Features file name | Any string |
"-o" associated align qualifiers
-aformat3 -aformat_o | string | Alignment format | Any string | fasta
-aextension3 -aextension_o | string | File name extension | Any string |
-adirectory3 -adirectory_o | string | Output directory | Any string |
-aname3 -aname_o | string | Base file name | Any string |
-awidth3 -awidth_o | integer | Alignment width | Any integer value | 0
-aaccshow3 -aaccshow_o | boolean | Show accession number in the header | Boolean value Yes/No | N
-adesshow3 -adesshow_o | boolean | Show description in the header | Boolean value Yes/No | N
-ausashow3 -ausashow_o | boolean | Show the full USA in the alignment | Boolean value Yes/No | N
-aglobal3 -aglobal_o | boolean | Show the full sequence in alignment | Boolean value Yes/No | N
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.

ehmmalign reads any normal sequence USAs.

### Input files for usage example

### File: ../ehmmcalibrate-ex-keep/globino.hmm

    HMMER2.0  [2.3.2]
    NAME  globins50
    LENG  143
    ALPH  Amino
    RF    no
    CS    no
    MAP   yes
    COM   /shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf
    COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm
    NSEQ  50
    DATE  Thu Jan  7 16:37:52 2010
    CKSUM 9858
    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   -35.959286   0.267496
    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
             -450      *  -1900
         1    591  -1587    159   1351  -1874   -201    151  -1600    998  -1591   -693    389  -1272    595     42    -31     27   -693  -1797  -1134    14
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378   -450      *
         2   -926  -2616   2221   2269  -2845  -1178   -325  -2678   -300  -2596  -1810    220  -1592    939   -974   -671   -939  -2204  -2785  -1925    15
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         3   -638  -1715   -680    497  -2043  -1540     23  -1671   2380  -1641   -840   -222  -1595    437   1040   -564   -523  -1363   2124  -1313    16
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         4    829  -1571    -37    660  -1856   -873    152  -1578    894  -1573   -678    769  -1273   1284     58    224    447  -1175  -1782  -1125    17
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         5    369   -433   -475    286   -974  -1312    -19   -412    664    398    406   1030  -1394    388   -214   -261     85   -166  -1227   -725    18
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         6  -1291   -884  -3696  -3261  -1137  -3425  -2802   2322  -3066    111     19  -3028  -3275  -2855  -3100  -2670  -1269   2738  -2450  -2062    19
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         7    157   -413   -236    316  -1387  -1231     89   -863   1084   -431   -348    910  -1319    635    297     15    704   -483  -1497   -922    20
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         8    770  -1431    -43    459  -1751   -340     78  -1449    440  -1497   -631    866  -1302    825    -51    953    364  -1076  -1750  -1121    21
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
         9    420   -186  -2172  -1577      8  -1818   -694   1477  -1281    760    614  -1299  -1867  -1001  -1262   -189    -12   1401   -722   -364    22
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
        10   -961   -879  -2277  -1821   1366  -2213   -204   -399  -1500   -130    -39  -1427  -2266  -1186  -1511   -159   -913   -367   4721   1177    23
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
        11    -48  -1782    809    844  -2073   1456      8  -1811    315  -1803   -932    180  -1365    921   -218    173   -115  -1399  -2018  -1327    24

      [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
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       128   -415  -1926   1575   1399  -2219  -1163     17  -1983    527  -1929  -1039    341  -1367   1597   -212    257   -222  -1536  -2109  -1387   144
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       129   -529  -1434   -629   -143  -1926   -626   -171  -1460   2679  -1597   -839   -309  -1599    207    317   -530   -510   -130  -1840  -1369   145
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       130    811   -397  -2389  -1807   1883  -2039   -907    594  -1512   1077    687  -1532  -2065  -1201  -1483  -1125   -465   1067   -843   -472   146
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       131   -241   -102  -2327  -1710    724  -1767   -616    650  -1363   1074   1765   -718  -1809  -1026  -1252   -842   -181   1331   -541    695   147
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       132    723     95    385    823  -1820  -1168    167  -1540    875  -1362   -644    320  -1261    810    246    693    -67  -1141  -1753  -1098   148
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       133    551   -430  -1049   -481   -442    469   -241    465   -313    133    947   -411  -1543    197   -587   -146    202    522   -843   -429   149
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       134  -1086   -777  -3351  -2800    816  -2898  -1861   1501  -2515   1149    586  -2483  -2775  -2108  -2400  -2046  -1030   2380  -1511  -1216   150
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       135   1393   1409   -876   -345   -997   -525   -315   -590   -198   -847   -109   -420  -1441    -97    412    766   -130    139  -1306   -858   151
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       136     98  -1299     36    365  -1495  -1211   1241   -404    523   -952   -426   1174  -1303    511    -18    347    882   -853  -1566   -970   152
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       137   1308   -787    564   -132   -966  -1332   -203   -362    -49   -395    -57   -305  -1481     49   -437   -190   -182   1020  -1282   -802   153
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       138  -1746  -1358  -3897  -3341   -216  -3621  -2478   1774  -3040   2442   1157  -3189  -3229  -2422  -2853  -2824  -1659    392  -1720  -1647   154
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       139   1176  -1289   -179    534  -1606   -607     34  -1278    734  -1372   -534     44  -1325    433    -89    521    826   -941  -1666  -1072   155
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
       140    602  -1500   -135    850  -1753  -1214   1951  -1452    838  -1484    431    118  -1306    555    347    489   -153  -1085  -1723  -1092   156
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -22  -6602  -7644   -894  -1115   -701  -1378      *      *
       141    351  -1646   -165    546  -1976   -498     46  -1667   2193  -1662   -798     35  -1405    476    311    -73   -306  -1287  -1859  -1254   157
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -23  -6561  -7603   -894  -1115   -701  -1378      *      *
       142  -1995  -1606  -3095  -2870   1739  -3015    -98  -1012  -2520   -730    655  -1990  -2962  -1884  -2326  -2167  -1915  -1128    548   4089   158
         -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
         -    -25  -6455  -7497   -894  -1115   -701  -1378      *      *
       143   -253  -1373   -267    301   -911   -565   1956   -450   1188  -1330   -497     33  -1352    502   1358   -205   -184   -941  -1604  -1026   159
         -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *
         -      *      *      *      *      *      *      *      *      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

ehmmalign 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

    >BAHG_VITSP
    .................mldqQTINIIKATV.PV...L.....K...E...H...GV.T.
    ....I...TTTFYKN..LFAKHPEVRPLFDMGRQESL-------..EQPKALAMTVLAAA
    QN-IENLPA......ILPAVKKIAVKH..CQAG-..VAAAHYPIV.GQELLGAIKEV.L.
    G.D.AATDDILDAWGKAYGVIADVFIQVEAdlyaqave
    >GLB1_ANABR
    .........psvqgaaaqltaDVKKDLRDSW.KV...I.....G...S...D...KK.G.
    ....N...GVALMTT..LFADNQETIGYFKRLGNVSQ---GMAN..DKLRGHSITLMYAL
    QNFIDQLDNt...ddLVCVVEKFAVNH..ITR-K..ISAAEFGKI.NGPIKKVLAS-.-.
    -.K.NFGDKYANAWAKLVAVVQAAL-----........
    >GLB1_ARTSX
    ..........ervdpitglsgLEKNAILDTW.GK...V.....R...G...N...LQ.E.
    ....V...GKATFGK..LFAAHPEYQQMFRFFQGVQL-AFLVQS..PKFAAHTQRVVSAL
    DQTLLALNRps..dqFVYMIKELGLDH..INRGT..-DRSFVEYL.KESL-----GD.S.
    V.D.EFT------VQSFGEVIVNFLNEGLRqa......
    >GLB1_CALSO
    ..................vsaNDIKNVQDTW.GK...L.....Y...D...Q...WD.A.
    ....V..hASKFYNK..LFKDSEDISEAFVKAGT---GSGIAMK..RQALVFGA-ILQEF
    VANLNDPTA......LTLKIKGLCATH..KTRGI..TNMELFAFA.LADLVAYMGTT.I.
    S.-.-FTAAQKASWTAVNDVILHQMSSYFAtva.....
    >GLB1_CHITH
    .................gpsgDQIAAAKASW.NT...V.....-...-...-...-K.N.
    ....N...QVDILYA..VFKANPDIQTAFSQFAG-KDLDSIKGT..PDFSKHAGRVVGLF
    SEVMDLLGNdantptILAKAKDFGKSH..--KSR..ASPAQLDNF.RKSLVVYLKGA.-.
    -.T.KWDSAVESSWAPVLDFVFSTLKNEL-........
    >GLB1_GLYDI
    .................glsaAQRQVIAATW.KD...I.....A...Ga.dN...GA.G.
    ....V...GKDCLIK..FLSAHPQMAAVFGFSGA--------SD..PGVAALGAKVLAQI
    GVAVSHLGDe...gkMVAQMKAVGVRHkgYGNKH..IKAQYFEPL.GASLLSAMEHR.I.
    G.G.KMNAAAKDAWAAAYADISGALISGLQs.......
    >GLB1_LUMTE
    .............eclvteglKVKLQWASAF.GH...A.....-...H...Q...RV.A.
    ....F...GLELWKG..ILREHPEIKAPFSRVRG-DN----IYS..PQFGAHSQRVLSGL
    DITISMLDTp...dmLAAQLAHLKVQH..VER-N..LKPEFFDIF.LKHLLHVLGDR.L.
    G.T.HFDF---GAWHDCVDQIIDGIKD--I........
    >GLB1_MORMR
    ........pivdsgsvsplsdAEKNKIRAAW.DL...V.....Y...K...D...YE.K.
    ....T...GVDILVK..FFTGTPAAQAFFPKFKGLTTADDLKQS..SDVRWHAERIINAV
    NDAVKSMDDt...ekMSMKLKELSIKH..AQSFY..VDRQYFKVL.AGII-------.-.
    -.A.DTTAPGDAGFEKLMSMICILLSSAY-........
    >GLB1_PARCH
    .......ggtlaiqshgdltlAQKKIVRKTW.HQ...L.....M...R...N...KT.S.
    ....F...VTDLFIR..IFAYDPAAQNKFPQMAGMSA-SQLRSS..RQMQAHAIRVSSIM
    SEYIEELDSd....iLPELLATLARTH..-DLNK..VGPAHYDLF.AKVLMEALQAE.L.
    G.S.DFNQKTRDSWAKAFSIVQAVLLVKHG........
    >GLB1_PETMA
    ........pivdsgsvpaltaAEKATIRTAW.AP...V.....Y...A...K...YQ.S.
    ....T...GVDILIK..FFTSNPAAQAFFPKFQGLTSADQLKKS..MDVRWHAERIINAV
    NDAVVAMDDt...ekMSLKLRELSGKH..AKSFQ..VDPQYFKVL.AAVI-------.-.
    -.V.DTVLPGDAGLEKLMSMICILLRSSY-........

      [Part of this file has been deleted for brevity]

    P.G.DFGADAQGAMKKALELFRNDMAAKYKelgfqg..
    >MYG_SHEEP
    .................glsdGEWQLVLNAW.GK...V.....E...A...D...VA.G.
    ....H...GQEVLIR..LFTGHPETLEKFDKFKHLKTEAEMKAS..EDLKKHGNTVLTAL
    GGILKKKGH......HEAEVKHLAESH..ANKHK..IPVKYLEFI.SDAIIHVLHAK.H.
    P.S.NFGADAQGAMSKALELFRNDMAAEYKvlgfqg..
    >MYG_SPAEH
    .................glsdGEWQLVLNVW.GK...V.....E...G...D...LA.G.
    ....H...GQEVLIK..LFKNHPETLEKFDKFKHLKSEDEMKGS..EDLKKHGNTVLTAL
    GGILKKKGQ......HAAEIQPLAQSH..ATKHK..IPIKYLEFI.SEAIIQVLQSK.H.
    P.G.DFGADAQGAMSKALELFRNDIAAKYKelgfqg..
    >MYG_TACAC
    .................glsdGEWQLVLKVW.GK...V.....E...T...D...IT.G.
    ....H...GQDVLIR..LFKTHPETLEKFDKFKHLKTEDEMKAS..ADLKKHGGVVLTAL
    GSILKKKGQ......HEAELKPLAQSH..ATKHK..ISIKFLEFI.SEAIIHVLQSK.H.
    S.A.DFGADAQAAMGKALELFRNDMATKYKefgfqg..
    >MYG_THUAL
    .....................ADFDAVLKCW.GP...V.....E...A...D...YT.T.
    ....M...GGLVLTR..LFKEHPETQKLFPKFAGIAQ-ADIAGN..AAISAHGATVLKKL
    GELLKAKGS......HAAILKPLANSH..ATKHK..IPINNFKLI.SEVLVKVMHEK.A.
    G.-.-LDAGGQTALRNVMGIIIADLEANYKelgfsg..
    >MYG_TUPGL
    .................glsdGEWQLVLNVW.GK...V.....E...A...D...VA.G.
    ....H...GQEVLIR..LFKGHPETLEKFDKFKHLKTEDEMKAS..EDLKKHGNTVLSAL
    GGILKKKGQ......HEAEIKPLAQSH..ATKHK..IPVKYLEFI.SEAIIQVLQSK.H.
    P.G.DFGADAQAAMSKALELFRNDIAAKYKelgfqg..
    >MYG_TURTR
    .................glsdGEWQLVLNVW.GK...V.....E...A...D...LA.G.
    ....H...GQDVLIR..LFKGHPETLEKFDKFKHLKTEADMKAS..EDLKKHGNTVLTAL
    GAILKKKGH......HDAELKPLAQSH..ATKHK..IPIKYLEFI.SEAIIHVLHSR.H.
    P.A.EFGADAQGAMNKALELFRKDIAAKYKelgfhg..
    >MYG_VARVA
    .................glsdEEWKKVVDIW.GK...V.....E...P...D...LP.S.
    ....H...GQEVIIR..MFQNHPETQDRFAKFKNLKTLDEMKNS..EDLKKHGTTVLTAL
    GRILKQKGH......HEAEIAPLAQTH..ANTHK..IPIKYLEFI.CEVIVGVIAEK.H.
    S.A.DFGADSQEAMRKALELFRNDMASRYKelgfqg..
    >MYG_VULCH
    .................glsdGEWQLVLNIW.GK...V.....E...T...D...LA.G.
    ....H...GQEVLIR..LFKNHPETLDKFDKFKHLKTEDEMKGS..EDLKKHGNTVLTAL
    GGILKKKGH......HEAELKPLAQSH..ATKHK..IPVKYLEFI.SDAIIQVLQSK.H.
    S.G.DFHADTEAAMKKALELFRNDIAAKYKelgfqg..
    >MYG_ZALCA
    .................glsdGEWQLVLNIW.GK...V.....E...A...D...LV.G.
    ....H...GQEVLIR..LFKGHPETLEKFDKFKHLKSEDEMKRS..EDLKKHGKTVLTAL
    GGILKKKGH......HDAELKPLAQSH..ATKHK..IPIKYLEFI.SEAIIHVLQSK.H.
    P.G.DFGADTHAAMKKALELFRNDIAAKYRelgfqg..
    >MYG_ZIPCA
    .................glseAEWQLVLHVW.AK...V.....E...A...D...LS.G.
    ....H...GQEILIR..LFKGHPETLEKFDKFKHLKSEAEMKAS..EDLKKHGHTVLTAL
    GGILKKKGH......HEAELKPLAQSH..ATKHK..IPIKYLEFI.SDAIIHVLHSR.H.
    P.S.DFGADAQAAMTKALELFRKDIAAKYKelgfhg..

## Data files

None.

## Notes

### 1. Command-line arguments

The following original HMMER options are not supported:

    -h         : Use -help to get help information instead.
    -informat  : All common sequence file formats are supported automatically.
    -oneline   : Alignment format output is specified via the ACD file and /
                 or the -aformat command line qualifier.
    -outformat : Alignment format output is specified via the ACD file and / or
                 the -aformat command line qualifier.

### 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

### Sequence input

ehmmalign makes a temporary local copy of its input sequence data. You must ensure there is sufficient disk space for this in the directory that ehmmalign is run.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
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
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.

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. Jon Ison (jison © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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.