                                   etmhmm



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Function

   Reports transmembrane helices

Description

   Prediction of transmembrane helices in proteins.

Usage

   Here is a sample session with etmhmm


% etmhmm
Reports transmembrane helices
Input (aligned) protein sequence set: 5h2a_crigr.fsa
Output file [5h2a_crigr.etmhmm]:


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

Command line arguments

Reports transmembrane helices
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein sequence set filename and
                                  optional format, or reference (input USA)
  [-outfile]           outfile    [*.etmhmm] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -html               boolean    [N] Produce html output
   -short              boolean    [N] Produce short output
   -plot               boolean    [N] Produce graphical output
   -one                boolean    [N] Use version 1 model file

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   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


Input file format

   etmhmm reads any normal sequence USAs.

  Input files for usage example

  File: 5h2a_crigr.fsa

>5H2A_CRIGR you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP
LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL
PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV

Output file format

  Output files for usage example

  File: 5h2a_crigr.etmhmm

# 5H2A_CRIGR Length: 471
# 5H2A_CRIGR Number of predicted TMHs:  7
# 5H2A_CRIGR Exp number of AAs in TMHs: 159.47336
# 5H2A_CRIGR Exp number, first 60 AAs:  0.01677
# 5H2A_CRIGR Total prob of N-in:        0.00629
5H2A_CRIGR      TMHMM2.0        outside      1    76
5H2A_CRIGR      TMHMM2.0        TMhelix     77    99
5H2A_CRIGR      TMHMM2.0        inside     100   111
5H2A_CRIGR      TMHMM2.0        TMhelix    112   134
5H2A_CRIGR      TMHMM2.0        outside    135   148
5H2A_CRIGR      TMHMM2.0        TMhelix    149   171
5H2A_CRIGR      TMHMM2.0        inside     172   191
5H2A_CRIGR      TMHMM2.0        TMhelix    192   214
5H2A_CRIGR      TMHMM2.0        outside    215   233
5H2A_CRIGR      TMHMM2.0        TMhelix    234   256
5H2A_CRIGR      TMHMM2.0        inside     257   324
5H2A_CRIGR      TMHMM2.0        TMhelix    325   347
5H2A_CRIGR      TMHMM2.0        outside    348   356
5H2A_CRIGR      TMHMM2.0        TMhelix    357   379
5H2A_CRIGR      TMHMM2.0        inside     380   471

Data files

   None.

Notes

   None.

References

    1. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L.
       Sonnhammer: Predicting Transmembrane Protein Topology with a Hidden
       Markov Model: Application to Complete Genomes. J. Mol. Biol.
       305:567-580, 2001.
    2. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh: A hidden
       Markov model for predicting transmembrane helices in protein
       sequences. In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on
       Intelligent Systems for Molecular Biology, pages 175-182. AAAI
       Press, 1998.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                    Program name                         Description
                    echlorop     Report presence of chloroplast transit peptides
                    elipop       Predict lipoproteins
                    esignalp     Report protein signal cleavage sites
                    sigcleave    Report on signal cleavage sites in a protein sequence
                    siggenlig    Generate ligand-binding signatures from a CON file
                    sigscan      Generate hits (DHF file) from a signature search
                    tmap         Predict and plot transmembrane segments in protein sequences
                    topo         Draw an image of a transmembrane protein

Author(s)

                    This program is an EMBOSS wrapper for a program written by the CBS
                    group http://www.cbs.dtu.dk/index.shtml

                    The original CBS group application must be licensed and installed to
                    use this wrapper.

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

History

Target users

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

Comments

                    None
