kphobius

Function

Predicts transmembrance topology and signal peptides using Phobius

Description

kphobius predicts transmembrance topology and signal peptides from the amino acid sequence of a protein utilizing Phobius. Phobius predicts a combined protein topolgy and signal peptide. The predictor is based on a hidden Markovmodel (HMM) that models the different sequence regions of a signal peptide and the different regions of a transmembrane protein in a series ofinterconnected states.

kphobius utilizes Phobius SOAP service provided by EBI (European Bioinformatics Institute). Original web-service is located at the following URL:

http://www.ebi.ac.uk/Tools/phobius/

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kphobius is thus an interface of "runPhobius" method included in KBWS SOAP service.
This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


  Here is a sample session with kphobius

% kphobius
Predicts transmembrance topology and signal peptides using Phobius
Input protein sequence(s): swissprot:MTH_DROME
Output file [mth_drome.kphobius]: 

ID   MTH_DROME
FT   SIGNAL        1     24       
FT   DOMAIN        1      3       N-REGION.
FT   DOMAIN        4     19       H-REGION.
FT   DOMAIN       20     24       C-REGION.
FT   DOMAIN       25    218       NON CYTOPLASMIC.
FT   TRANSMEM    219    238       
FT   DOMAIN      239    249       CYTOPLASMIC.
FT   TRANSMEM    250    269       
FT   DOMAIN      270    280       NON CYTOPLASMIC.
FT   TRANSMEM    281    302       
FT   DOMAIN      303    321       CYTOPLASMIC.
FT   TRANSMEM    322    342       
FT   DOMAIN      343    371       NON CYTOPLASMIC.
FT   TRANSMEM    372    391       
FT   DOMAIN      392    421       CYTOPLASMIC.
FT   TRANSMEM    422    439       
FT   DOMAIN      440    450       NON CYTOPLASMIC.
FT   TRANSMEM    451    476       
FT   DOMAIN      477    514       CYTOPLASMIC.
//

	  

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall Protein sequence(s) filename and optional format, or reference (input USA) Readable protein sequence(s) Required
[-outfile]
(Parameter 2)
outfile Output file name Phobius output file <*>.kphobius
Additional (Optional) qualifiers
-outputformat string The output format: 'long', 'short', 'raw' or 'grp' Any string grp
Advanced (Unprompted) qualifiers
(none)

Input file format

kphobius can use any genome sequence data that seqret can read.

Output file format

The output from kphobius has three format. Default format (long) is a list of the location of the predicted transmembrane helices, the predicted location of the intervening loop regions and signal peptide.

Data files

None.

Notes

None.

References

      Kåll, K., et al.,(2004) A combined transmembrane topology and signal peptide
      prediction method, Journal of Molecular Biology, 338(5), 1027-1036.

      Kåll, K., et al.,(2005) An HMM posterior decoder for sequence feature prediction
      that includes homology information, Bioinformatics, 21, i251-i257.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org)
Institute for Advanced Biosciences, Keio University
252-8520 Japan

History

2009 - Written by Kazuki Oshita
Mar 2013 - Update document by Kazuki Oshita

Target users

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

Comments

None.