                                   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) 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:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) 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
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   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
   antigenic        Finds antigenic sites in proteins
   digest           Reports on protein proteolytic enzyme or reagent cleavage sites
   echlorop         Reports presence of chloroplast transit peptides
   eiprscan         Motif detection
   elipop           Prediction of lipoproteins
   emast            Motif detection
   ememe            Multiple EM for Motif Elicitation
   ememetext        Multiple EM for Motif Elicitation. Text file only
   enetnglyc        Reports N-glycosylation sites in human proteins
   enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian
                    proteins
   enetphos         Reports ser, thr and tyr phosphorylation sites in eukaryotic
                    proteins
   epestfind        Finds PEST motifs as potential proteolytic cleavage sites
   eprop            Reports propeptide cleavage sites in proteins
   esignalp         Reports protein signal cleavage sites
   eyinoyang        Reports O-(beta)-GlcNAc attachment sites
   fuzzpro          Search for patterns in protein sequences
   fuzztran         Search for patterns in protein sequences (translated)
   helixturnhelix   Identify nucleic acid-binding motifs in protein
                    sequences
   oddcomp          Identify proteins with specified sequence word composition
   omeme            Motif detection
   patmatdb         Searches protein sequences with a sequence motif
   patmatmotifs     Scan a protein sequence with motifs from the PROSITE
                    database
   pepcoil          Predicts coiled coil regions in protein sequences
   preg             Regular expression search of protein sequence(s)
   pscan            Scans protein sequence(s) with fingerprints from the PRINTS
                    database
   sigcleave        Reports on signal cleavage sites in a protein sequence

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.

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

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

Target users

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

Comments

   None
