kwolfpsort

Function

Predicts protein localization for WoLF PSORT

Description

kwolfpsort predicts the subcellular localization sites of proteins based on their amino acid sequences utilizing WoLF PSORT. WoLF PSORT is a mafor extension to the PSORT II program, and makes predictions based on both known sorting signal motifs and some correlative sequene features such as amino acid content.

kwolfpsort utilize WoLF PSORT web service provided by PSORT WWW Server. Original web-service is located at the following URL:

http://wolfpsort.org/

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. kwolfpsort is thus an interface of "runWolfPsort" 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 kwolfpsort

% kwolfpsort
Predicts protein localization for WoLF PSORT
Input protein sequence(s): swissprot:ARFB_ARATH
organism type (animal/plant/fungi): animal
Output file [arfb_arath.kwolfpsort]: 

32 Nearest Neighbors
id	site	distance	identity	comments	
PHC1_HUMAN	nucl 50.2 16%	[Uniprot] SWISS-PROT45:Nuclear. GO:0005634; C:nucleus; Evidence:TAS.
PCAP_HUMAN	cyto_nucl 52.6 12%	[Uniprot] SWISS-PROT45:Cytoplasmic and nuclear.
PHC1_MOUSE	nucl 52.9 15%	[Uniprot] SWISS-PROT45:Nuclear. GO:0005634; C:nucleus; Evidence:IDA.
P73_HUMAN	nucl 56.3 15%	[Uniprot] SWISS-PROT45:Nuclear.
SOX5_MOUSE	nucl 56.5 12%	[Uniprot] SWISS-PROT45:Nuclear.
NCO2_XENLA	nucl 57.0 13%	[Uniprot] SWISS-PROT45:Nuclear.
RBL2_HUMAN	nucl 57.7 14%	[Uniprot] SWISS-PROT45:Nuclear.
MLPH_HUMAN	cyto 61.4 15%	[Uniprot] SWISS-PROT45:Cytoplasmic.
FXR1_XENLA	cyto 61.5 14%	[Uniprot] SWISS-PROT45:Cytoplasmic.
PTN8_MOUSE	cyto 62.6 12%	[Uniprot] SWISS-PROT45:Cytoplasmic.
P73_CERAE	nucl 63.3 15%	[Uniprot] SWISS-PROT45:Nuclear.
ORC2_XENLA	nucl 63.8 14%	[Uniprot] SWISS-PROT45:Nuclear.
UBP4_HUMAN	cyto 64.0 13%	[Uniprot] SWISS-PROT45:Cytoplasmic. GO:0005634; C:nucleus; Evidence:TAS.
RGP2_HUMAN	golg 64.1 13%	[Uniprot] SWISS-PROT45:Associated with Golgi membranes.
MYC2_CYPCA	nucl 64.3 12%	[Uniprot] SWISS-PROT45:Nuclear.
UB36_HUMAN	nucl 64.3 14%	[Uniprot] SWISS-PROT45:Nuclear; nucleolar.
SOX2_XENLA	nucl 64.8 11%	[Uniprot] SWISS-PROT45:Nuclear.
DYRB_HUMAN	nucl 65.0 15%	[Uniprot] SWISS-PROT45:Nuclear. GO:0005634; C:nucleus; Evidence:TAS.
SOX2_SHEEP	nucl 65.3 11%	[Uniprot] SWISS-PROT45:Nuclear.
DYRB_MOUSE	nucl 65.6 15%	[Uniprot] SWISS-PROT45:Nuclear.
KBF2_HUMAN	cyto_nucl 66.3 14%	[Uniprot] SWISS-PROT45:Nuclear, but also found in the cytoplasm in an inactive form complexed to an inhibitor (I-kappa-B).
SOX2_CHICK	nucl 67.0 10%	[Uniprot] SWISS-PROT45:Nuclear.
AKA8_RAT	nucl 67.8 14%	[Uniprot] SWISS-PROT45:Nuclear. Associated with the nuclear matrix. Redistributed and detached from condensed chromatin during mitosis (By similarity).
T7L2_HUMAN	nucl 68.2 15%	[Uniprot] SWISS-PROT45:Nuclear.
TLE3_MOUSE	nucl 68.4 12%	[Uniprot] SWISS-PROT45:Nuclear.
CSP7_HUMAN	nucl 68.4 16%	[Uniprot] SWISS-PROT45:Nuclear.
SOX3_XENLA	nucl 68.7  9%	[Uniprot] SWISS-PROT45:Nuclear.
PEXE_HUMAN	pero 68.7 12%	[Uniprot] SWISS-PROT45:Peroxisomal; membrane-associated. Outer face. GO:0005777; C:peroxisome; Evidence:TAS.
LI36_CAEEL	nucl 69.1 13%	[Uniprot] SWISS-PROT45:Nuclear.
CCT1_HUMAN	nucl 69.2 15%	[Uniprot] SWISS-PROT45:Nuclear.
BAB1_DROME	nucl 69.8 14%	[Uniprot] SWISS-PROT45:Nuclear. GO:0005634; C:nucleus; Evidence:IDA.
SX19_BRARE	nucl 69.9 10%	[Uniprot] SWISS-PROT45:Nuclear.

	    

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
[-org]
(Parameter 2)
string organism type (animal/plant/fungi) Any string Required
[-outfile]
(Parameter 3)
outfile Output file name Output file <*>.kwolfpsort
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

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

Output file format

The output of kwolfpsort is general WoLF PSORT output format.

Data files

None.

Notes

None.

References

	Horton, P., et al.,(2006) Protein Subcelluar Localization Prediction
	with WoLF PSORT, Proceedings of the 4th Annual Asia Pacific Bioinformatics
	Conference APBC06, 39-48.

	Horton, P., et al.,(2007) WoLF PSORT: Protein Localization Predictor
	Nucleic Acids Research Web Server issue, 35, 585-587.
      

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
kpsortb Predicts protein localization for PSORT B
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

Target users

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

Comments

None.