kpsortb

Function

Predicts protein localization for PSORTB

Description

kpsortb predicts protein localization sites utilizing PSORTb.

PSORTb analyzes the subcellular localization of proteins from amino acid sequence. PSORTb consists of multiple analytical modules and classifying a protein as either belonging or not belonging to a particular localization site for various sequence features.

kpsortb utilizes PSORT WWW Server provided by www.psort.org. This service is based on PSORTb v.2.0. PSORTb v.2.0 is updated from PSORT-B v.1.1. Differences between those include "updated several algorithms", "utilizing a probabilistic system" and etc. Original web-service is located at the following URL:

http://www.psort.org/psortb/

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. kpsortb is thus an interface of "runPsortb" 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 kpsortb

% kpsortb
prediction protein localization sets for bacterial sequences
Input protein sequence(s): swissprot:P50930
negative or positive [negative]: 
Output file [17kd_ricpa.kpsortb]: stdout

SeqID: YourSeq 
Analysis Report:
CMSVM-            Unknown                       [No details]
CytoSVM-          Unknown                       [No details]
ECSVM-            Unknown                       [No details]
HMMTOP-           CytoplasmicMembrane           [3 internal helices found]
Motif-            Unknown                       [No motifs found]
OMPMotif-         Unknown                       [No motifs found]
OMSVM-            Unknown                       [No details]
PPSVM-            Unknown                       [No details]
Profile-          Unknown                       [No matches to profiles found]
SCL-BLAST-        Unknown                       [No matches against database]
SCL-BLASTe-       Unknown                       [No matches against database]
Signal-           Unknown                       [No signal peptide detected]
Localization Scores:
Cytoplasmic            0.04
CytoplasmicMembrane    9.46
Periplasmic            0.07
OuterMembrane          0.18
Extracellular          0.25
Final Prediction:
CytoplasmicMembrane    9.46
-------------------------------------------------------------------------------

	  

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 sequence(s) Required
[-gram]
(Parameter 2)
string Choose GRAM stain from 'negative' or 'positive' 'negative' or 'positive' negative
[-outfile]
(Parameter 3)
outfile Standard PSORTB output filename Output file <*>.kpsortb
Additional (Optional) qualifiers
-format string Output file format. 'normal': general output format, 'short' : Short Format (tab delimited), 'long' : Long Format (tab delimited) Any string normal
Advanced (Unprompted) qualifiers
(none)

Input file format

kpsortb can use any amino acid sequence data that seqret can read.

Output file format

The output from kpsortb is general PSORTb output format.

Data files

None.

Notes

None.

References

      Gardy, JL., et al.,(2003) PSORT-B: improving protein subcellular
      localization prediction for Gram-negative bacteria, Nucleic Acids Research,
      31(13), 3613-3617.

      Gardy, JL., et al.,(2005) PSORTb v.2.0: expanded prediction of
      bacterial protein subcellular localization and insights gained from
      comparative proteome analysis, Bioinformatics, 21(5), 617-623.

      Yu, NY., et al.,(2010) PSORTb 3.0: improved protein subcellular localization
      prediction with refined localization subcategories and predictive capabilities
      for all prokaryotes, Bioinformatics, 26(13), 1608-1615.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
kpsort Predicts protein localization for PSORT
kpsort2 Predicts protein localization for PSORT2
kwolfpsort Predicts protein localization for WoLF PSORT
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 Kauzki Oshita

Target users

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

Comments

None.