| ehmmpfam

## Wiki

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

Please help by correcting and extending the Wiki pages.

## Function

Search one or more sequences against 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:
ehmmpfam [options] hmmfile seqfile outfile

The outfile parameter is new to EMBASSY HMMER.

hmmpfam reads a sequence file and compares each sequence in it, one at a time, against all the HMMs in a file looking for signifcantly similar sequence matches. hmmfile will be looked for first in the current working directory, then in a directory named by the environment variable HMMERDB. This lets administrators install HMM library(s) such as Pfam in a common location. There is a separate output report (written to file for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the -domE and -domT options.

## 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 ehmmpfam

    % ehmmpfam ../ehmmcalibrate-ex2-keep/myhmmso 7LES_DROME myhmmso.ehmmpfam -A 10 -E 10
    Search one or more sequences against an HMM database.

    /shared/software/bin/hmmpfam -A 10 -E 10.000000 -T -1000000.000000 -Z 59021 --domE 1000000.000000 --domT -1000000.000000  --informat FASTA ../ehmmcalibrate-ex2-keep/myhmmso ./ehmmpfam-1234567890.1234 > myhmmso.ehmmpfam

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).

    Search one or more sequences against an HMM database.
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers:
      [-hmmfile]           infile     File of HMMs.
      [-seqfile]           seqall     File of sequences.
       -a                  integer    [100] Limits the alignment output to the
                                      best scoring domains. -A0 shuts off the
                                      alignment output and can be used to reduce
                                      the size of output files. (Any integer
                                      value)
       -e                  float      [10.] Set the E-value cutoff for the
                                      per-sequence ranked hit list to , where
                                       is a positive real number. The default
                                      is 10.0. Hits with E-values better than
                                      (less than) this threshold will be shown.
                                      (Any numeric value)
      [-outfile]           outfile    [*.ehmmpfam] There is a separate output
                                      report for each sequence in seqfile. This
                                      report consists of three sections: a ranked
                                      list of the best scoring HMMs, a list of the
                                      best scoring domains in order of their
                                      occurrence in the sequence, and alignments
                                      for all the best scoring domains.

       Additional (Optional) qualifiers:
       -nuc                boolean    [N] Specify that models and sequence are
                                      nucleic acid, not protein. Other HMMER
                                      programs autodetect this; but because of the
                                      order in which hmmpfam accesses data, it
                                      can't reliably determine the correct
                                      'alphabet' by itself.
       -t                  float      [-1000000.] Set the bit score cutoff for the
                                      per-sequence ranked hit list to , where
                                       is a real number. The default is
                                      negative infinity; by default, the threshold
                                      is controlled by E-value and not by bit
                                      score. Hits with bit scores better than
                                      (greater than) this threshold will be shown.
                                      (Any numeric value)
       -z                  integer    [59021] Calculate the E-value scores as if
                                      we had seen a sequence database of
                                      sequences. The default is arbitrarily set to
                                      59021, the size of Swissprot 34. (Any
                                      integer value)

       Advanced (Unprompted) qualifiers:
       -acc                boolean    [N] Report HMM accessions instead of names
                                      in the output reports. Useful for
                                      high-throughput annotation, where the data
                                      are being parsed for storage in a relational
                                      database.
       -compat             boolean    [N] Use the output format of HMMER 2.1.1,
                                      the 1998-2001 public release; provided so
                                      2.1.1 parsers don't have to be rewritten.
       -cpu                integer    [0] Sets the maximum number of CPUs that the
                                      program will run on. The default is to use
                                      all CPUs in the machine. Overrides the HMMER
                                      NCPU environment variable. Only affects
                                      threaded versions of HMMER (the default on
                                      most systems). (Any integer value)
       -cutga              boolean    [N] Use Pfam GA (gathering threshold) score
                                      cutoffs. Equivalent to -globT  -domT
                                      , but the GA1 and GA2 cutoffs are read
                                      from each HMM in the input HMM database
                                      individually. hmmbuild puts these cutoffs
                                      there if the alignment file was annotated in
                                      a Pfam-friendly alignment format (extended
                                      SELEX or Stockholm format) and the optional
                                      GA annotation line was present. If these
                                      cutoffs are not set in the HMM file, -cut ga
                                      doesn't work.
       -cuttc              boolean    [N] Use Pfam TC (trusted cutoff) score
                                      cutoffs. Equivalent to -globT  -domT
                                      , but the TC1 and TC2 cutoffs are read
                                      from each HMM in hmmfile individually.
                                      hmmbuild puts these cutoffs there if the
                                      alignment file was annotated in a
                                      Pfam-friendly alignment format (extended
                                      SELEX or Stockholm format) and the optional
                                      TC annotation line was present. If these
                                      cutoffs are not set in the HMM file, -cut tc
                                      doesn't work.
       -cutnc              boolean    [N] Use Pfam NC (noise cutoff) score
                                      cutoffs. Equivalent to -globT  -domT
                                      , but the NC1 and NC2 cutoffs are read
                                      from each HMM in hmmfile individually.
                                      hmmbuild puts these cutoffs there if the
                                      alignment file was annotated in a
                                      Pfam-friendly alignment format (extended
                                      SELEX or Stockholm format) and the optional
                                      NC annotation line was present. If these
                                      cutoffs are not set in the HMM file, -cut nc
                                      doesn't work.
       -dome               float      [1000000.] Set the E-value cutoff for the
                                      per-domain ranked hit list to , where
                                      is a positive real number. The default is
                                      infinity; by default, all domains in the
                                      sequences that passed the frst threshold
                                      will be reported in the second list, so that
                                      the number of domains reported in the
                                      per-sequence list is consistent with the
                                      number that appear in the per-domain list.
                                      (Any numeric value)
       -domt               float      [-1000000.] Set the bit score cutoff for the
                                      per-domain ranked hit list to , where
                                       is a real number. The default is
                                      negative infinity; by default, all domains
                                      in the sequences that passed the frst
                                      threshold will be reported in the second
                                      list, so that the number of domains reported
                                      in the per-sequence list is consistent with
                                      the number that appear in the per-domain
                                      list. Important note: only one domain in a
                                      sequence is absolutely controlled by this
                                      parameter, or by --domT. The second and
                                      subsequent domains in a sequence have a de
                                      facto bit score threshold of 0 because of
                                      the details of how HMMER works. HMMER
                                      requires at least one pass through the main
                                      model per sequence; to do more than one pass
                                      (more than one domain) the multidomain
                                      alignment must have a better score than the
                                      single domain alignment, and hence the extra
                                      domains must contribute positive score. See
                                      the Users' Guide for more detail. (Any
                                      numeric value)
       -forward            boolean    [N] Use the Forward algorithm instead of the
                                      Viterbi algorithm to determine the
                                      per-sequence scores. Per-domain scores are
                                      still determined by the Viterbi algorithm.
                                      Some have argued that Forward is a more
                                      sensitive algorithm for detecting remote
                                      sequence homologues; my experiments with
                                      HMMER have not confrmed this, however.
       -nulltwo            boolean    [N] Turn off the post hoc second null model.
                                      By default, each alignment is rescored by a
                                      postprocessing step that takes into account
                                      possible biased composition in either the
                                      HMM or the target sequence. This is almost
                                      essential in database searches, especially
                                      with local alignment models. There is a very
                                      small chance that this postprocessing might
                                      remove real matches, and in these cases
                                      --null2 may improve sensitivity at the
                                      expense of reducing specifcity by letting
                                      biased composition hits through.
       -pvm                boolean    [N] Run on a Parallel Virtual Machine (PVM).
                                      The PVM must already be running. The client
                                      program hmmpfam-pvm must be installed on
                                      all the PVM nodes. The HMM database hmmfile
                                      and an associated GSI index file hmmfile.gsi
                                      must also be installed on all the PVM
                                      nodes. (The GSI index is produced by the
                                      program hmmindex.) Because the PVM
                                      implementation is I/O bound, it is highly
                                      recommended that each node have a local copy
                                      of hmmfile rather than NFS mounting a
                                      shared copy. Optional PVM support must have
                                      been compiled into HMMER for -pvm to
                                      function.
       -xnu                boolean    [N] Turn on XNU filtering of target protein
                                      sequences. Has no effect on nucleic acid
                                      sequences. In trial experiments, -xnu
                                      appears to perform less well than the
                                      default post hoc null2 model.

       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

       "-outfile" associated qualifiers
       -odirectory3        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-hmmfile] (Parameter 1) | infile | File of HMMs. | Input file | Required
[-seqfile] (Parameter 2) | seqall | File of sequences. | Readable sequence(s) | Required
-a | integer | Limits the alignment output to the <n> best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files. | Any integer value | 100
-e | float | Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown. | Any numeric value | 10.
[-outfile] (Parameter 3) | outfile | There is a separate output report for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. | Output file | <*>.ehmmpfam
Additional (Optional) qualifiers
-nuc | boolean | Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can't reliably determine the correct 'alphabet' by itself. | Boolean value Yes/No | No
-t | float | Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown. | Any numeric value | -1000000.
-z | integer | Calculate the E-value scores as if we had seen a sequence database of <n> sequences. The default is arbitrarily set to 59021, the size of Swissprot 34. | Any integer value | 59021
Advanced (Unprompted) qualifiers
-acc | boolean | Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database. | Boolean value Yes/No | No
-compat | boolean | Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten. | Boolean value Yes/No | No
-cpu | integer | Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems). | Any integer value | 0
-cutga | boolean | Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT <GA1> -domT <GA2>, but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn't work. | Boolean value Yes/No | No
-cuttc | boolean | Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT <TC1> -domT <TC2>, but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn't work. | Boolean value Yes/No | No
-cutnc | boolean | Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT <NC1> -domT <NC2>, but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn't work. | Boolean value Yes/No | No
-dome | float | Set the E-value cutoff for the per-domain ranked hit list to <x>, where <x> is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. | Any numeric value | 1000000.
-domt | float | Set the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users' Guide for more detail. | Any numeric value | -1000000.
-forward | boolean | Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however. | Boolean value Yes/No | No
-nulltwo | boolean | Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases --null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through. | Boolean value Yes/No | No
-pvm | boolean | Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function. | Boolean value Yes/No | No
-xnu | boolean | Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model. | Boolean value Yes/No | No
Associated qualifiers
"-seqfile" associated seqall 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 |
"-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.

ehmmpfam reads any normal sequence USAs.

### Input files for usage example

### File: ../ehmmcalibrate-ex2-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 Jan  7 16:51:40 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
    //

### File: 7LES_DROME

    ID   7LES_DROME     STANDARD;      PRT;  2554 AA.
    AC   P13368;
    DT   01-JAN-1990 (Rel. 13, Created)
    DT   01-JAN-1990 (Rel. 13, Last sequence update)
    DT   01-NOV-1997 (Rel. 35, Last annotation update)
    DE   SEVENLESS PROTEIN (EC 2.7.1.112).
    GN   SEV.
    OS   Drosophila melanogaster (Fruit fly).
    OC   Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
    OC   Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
    OC   Ephydroidea; Drosophilidae; Drosophila.
    RN   [1]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=CANTON-S;
    RX   MEDLINE; 88282538.
    RA   BASLER K., HAFEN E.;
    RT   "Control of photoreceptor cell fate by the sevenless protein requires
    RT   a functional tyrosine kinase domain.";
    RL   Cell 54:299-311(1988).
    RN   [2]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=OREGON-R;
    RX   MEDLINE; 88329706.
    RA   BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
    RT   "Nucleotide sequence and structure of the sevenless gene of
    RT   Drosophila melanogaster.";
    RL   Genes Dev. 2:620-634(1988).
    RN   [3]
    RP   IDENTIFICATION OF FN-III REPEATS.
    RX   MEDLINE; 90199889.
    RA   NORTON P.A., HYNES R.O., RESS D.J.G.;
    RT   "Sevenless: seven found?";
    RL   Cell 61:15-16(1990).
    CC   -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
    CC       INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
    CC       LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
    CC       SURFACE OF THE NEIGHBORING R8 CELL.
    CC   -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
    CC       PROTEIN TYROSINE PHOSPHATE.
    CC   -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
    CC   -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
    CC       PROTEIN KINASES. SEVENLESS SUBFAMILY.
    CC   -!- SIMILARITY: CONTAINS 7 FIBRONECTIN TYPE III-LIKE DOMAINS.
    CC   -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
    CC       NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
    CC       NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
    CC   --------------------------------------------------------------------------
    CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
    CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
    CC   the European Bioinformatics Institute.  There are no  restrictions on  its

      [Part of this file has been deleted for brevity]

    FT   VARIANT    1703   1703       N -> H.
    FT   VARIANT    1730   1730       R -> K.
    FT   VARIANT    1731   1731       G -> E.
    FT   VARIANT    1741   1741       V -> M.
    FT   VARIANT    2271   2271       R -> C.
    FT   CONFLICT   1823   1823       E -> Q (IN REF. 2).
    SQ   SEQUENCE   2554 AA;  287107 MW;  1143D891 CRC32;
         MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
         SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
         CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
         SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
         KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
         QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
         LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
         LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
         NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
         TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
         SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
         ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
         QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
         SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
         KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
         VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
         PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
         CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
         GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
         PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
         VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
         AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
         DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
         TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
         EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
         RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
         GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
         DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
         LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
         VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
         PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
         AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
         GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
         GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
         RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
         HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
         LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
         GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
         SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
         HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
         DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
         LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
         HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
    //

## Output file format

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

### Output files for usage example

### File: myhmmso.ehmmpfam

    hmmpfam - search one or more sequences against HMM database
    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-ex2-keep/myhmmso
    Sequence file:            ./ehmmpfam-1234567890.1234
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

    Query sequence: 7LES_DROME
    Accession:      [none]
    Description:    P13368 SEVENLESS PROTEIN (EC 2.7.1.112).

    Scores for sequence family classification (score includes all domains):
    Model    Description                                    Score    E-value  N
    -------- -----------                                    -----    ------- ---
    pkinase  Protein kinase domain                          314.6    1.2e-90   1
    fn3      Fibronectin type III domain                    176.6      4e-49   6

    Parsed for domains:
    Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
    -------- ------- ----- -----    ----- -----      -----  -------
    fn3        1/6     437   522 ..     1    84 []    48.3  1.7e-10
    fn3        2/6     825   914 ..     1    84 []    13.4     0.09
    fn3        3/6    1292  1389 ..     1    84 []    15.9     0.05
    fn3        4/6    1799  1891 ..     1    84 []    63.5  4.5e-15
    fn3        5/6    1899  1978 ..     1    84 []    15.2     0.06
    fn3        6/6    1993  2107 ..     1    84 []    20.3    0.018
    pkinase    1/1    2209  2483 ..     1   294 []   314.6  1.2e-90

    Alignments of top-scoring domains:
    fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 1.7e-10
                    CS    C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
                       *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
                          P saP   + +++ ++ l ++W p +  ngpi+gY++++ +++ g+
      7LES_DROME   437    PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482

                    CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
                       wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                       + e+ vp    sy+++ L++gt+Y++ +  +n +G+Gp
      7LES_DROME   483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA    522

    fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 0.09
                    CS    CCCCCEEEEEECCTTCCEEEEECCC       CCCCCCCEEEEE.EC
                       *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
                           ++P  l++   ++  + +sW+ p++++ ++ + +   +Ye+++  +
      7LES_DROME   825    GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869

                    CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC  CCCC
                       knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*

      [Part of this file has been deleted for brevity]

                    CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
                       eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                       +++v g+ t ++++ L+P t+Y+ r+    ++++G++
      7LES_DROME  1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL    1978

    fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 0.018
                    CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
                       *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
                          Ps+P+ ++ + + +  ++++W++++++++pi  Y+++   ++++  +
      7LES_DROME  1993    PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038

                    CS                            CCCCEEECCCC CECECCEEEEE
                       ...........................wneltvpgttt.sytltgLkPgt
                       +++++++++++++ ++ +  +++   ++++l+  +tt  s++++ L   +
      7LES_DROME  2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088

                    CS CCCCEEEEEE CCC CCCC
                       eYevrVqAvn.ggG.GpeS<-*
                          +rV+A++ ++G Gp+S
      7LES_DROME  2089 LLLFRVRARSlEHGwGPYS    2107

    pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 1.2e-90
                       *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
                          ++ll+ lG+G+fG+Vy++++k+++++  ++VA+K l+k+++++ e
      7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253

                       flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
                       +l E+q++ +++H+NIvrl g++  + +++ l+mE+me GdL++ylr+ +
      7LES_DROME  2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302

                       ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
                        +++++++++  ls  e++ ++ ++++G +YL+++++vHRDL+ +N+L++
      7LES_DROME  2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352

                       en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
                       e +++++++ tvKi+DFGLAr++++++++++ + +  p+++m+PE  l +
      7LES_DROME  2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401

                       rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
                         +++++DvW++Gv+++E+lt g                         ++
      7LES_DROME  2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426

                       PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
                       P+         ++ +e+++++k+ g+rl +p+ c e l++Ll  c++ DP
      7LES_DROME  2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468

                       skRpGsatakeilnhpwf<-*
                       ++Rp   +++ + n +
      7LES_DROME  2469 WERP---SFRRCYNTLHA    2483

    //

## 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.
    -n         : Use -nuc 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

### Disk space requirements

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

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
ehmmalign | Align sequences to an HMM profile
ehmmbuild | Build a profile HMM from an alignment
ehmmcalibrate | Calibrate HMM search statistics
ehmmconvert | Convert between profile HMM file formats
ehmmemit | Generate sequences from a profile HMM
ehmmfetch | Retrieve an HMM from an HMM database
ehmmindex | Create a binary SSI index for an HMM database
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.