EMBOSS: kpathwayprojector manual

kpathwayprojector

Function

Mapping experimental data on PathwayProjector

Description

kpathwayprojector maps experimental data, such as transcriptomics, proteomics or metabolomics on Pathway Projector.

Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped.

Pathway Projector is provided by Institute for Advanced Biosciences. Original web service is located at the following URL:

http://www.g-language.org/PathwayProjector/

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. kprotpars is thus an interface of "map2PathwayProjector" 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://soap.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kprotpars

% kpathwayprojector
Mapping experimental data on PathwayProjector
Input (gapped) sequence(s): infile.dat
Jobid: kbws_12547145
***********

Pathway Projector's URL : http://ws.g-language.org/g4/main.cgi?diaAtabareaname=1&flag=6831094
Image File : http://soap.g-language.org/12547145.png

Command line arguments

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-infile] (Parameter 1)	infile	(no help text) infile value	Input file	2
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat

Organism:eco
pgk,red

Output file format

kpathwayprojector outputs two URLs.

Pathway Projector's URL : Direct link to Pathway Projector mapped your data.
Image File : Image of Pathway Map mapped on your data. This file is png format.

Data files

Notes

References

Warnings

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

Author(s)

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

History

2010 - Written by Kazuki Oshita

Target users

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