KEGGgraph 1.28.0 – A Graph Approach to KEGG PATHWAY in R and Bioconductor

KEGGgraph 1.28.0

:: DESCRIPTION

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

::DEVELOPER

Jitao David Zhang <jitao_david.zhang at roche.com>, Stefan Wiemann 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 KEGGgraph

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 1;25(11):1470-1. doi: 10.1093/bioinformatics/btp167. Epub 2009 Mar 23.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
Zhang JD, Wiemann S.

KATSURA 1.0.1 – KEGG Pathway Coverage & Expression Analysis

KATSURA 1.0.1

:: DESCRIPTION

Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.

::DEVELOPER

KATSURA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • JAVA

:: DOWNLOAD

KATSURA

:: MORE INFORMATION

This application is released under the GPL v3 License: View License

Citation:

  1. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010).
  2. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
  3. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

KEGGscape 0.7.0 – File Reader and Pathway Vsualizer for KEGG XML (KGML) files

KEGGscape 0.7.0

:: DESCRIPTION

KEGGscape is a pathway data integration and visualization app for Cytoscape.

::DEVELOPER

KEGGscape team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Cytoscape

:: DOWNLOAD

KEGGscape

:: MORE INFORMATION

Citation

KEGGscape: a Cytoscape app for pathway data integration.
Nishida K, Ono K, Kanaya S, Takahashi K.
F1000Res. 2014 Jul 1;3:144. doi: 10.12688/f1000research.4524.1

MicrobesFlux – Web Platform for Drafting Metabolic Models from the KEGG Database

MicrobesFlux

:: DESCRIPTION

MicrobesFlux is a web-based platform for generating and reconstructing metabolic models for annotated microorganisms.

::DEVELOPER

MicrobesFlux team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2012 Aug 2;6:94.
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.
Feng X1, Xu Y, Chen Y, Tang YJ.

KAAS 20140224 – KEGG Automatic Annotation Server

KAAS 20140224

:: DESCRIPTION

KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

::DEVELOPER

Kyoto University Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • ruby
  • NCBI
  • HMMER

:: DOWNLOAD

  KAAS

:: MORE INFORMATION

Citation

KAAS: an automatic genome annotation and pathway reconstruction server.
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5.

KEGGParser 20140324 – Parsing and Editing KEGG Pathway Maps in Matlab

KEGGParser 20140324

:: DESCRIPTION

KEGGParser is a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.

::DEVELOPER

 Arsen Arakelyan

:: SCREENSHOTS

KEGGParser

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • MatLab

:: DOWNLOAD

 KEGGParser

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):518-9. doi: 10.1093/bioinformatics/bts730. Epub 2013 Jan 3.
KEGGParser: parsing and editing KEGG pathway maps in Matlab.
Arakelyan A, Nersisyan L.

Pathway Projector – Zoomable Pathway Browser using KEGG Atlas

Pathway Projector

:: DESCRIPTION

The Pathway Projector was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities.

::DEVELOPER

PathwayProjector team

:: SCREENSHOTS

Pathwayprojector

:: REQUIREMENTS

  • Web Browser 
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M.
PLoS One. 2009 Nov 11;4(11):e7710. doi: 10.1371/journal.pone.0007710.

annot8r 1.1.1 – BLAST based GO-EC-KEGG Annotation

annot8r 1.1.1

:: DESCRIPTION

annot8r is a tool for the annotation of protein or nucleotide sequences from non model organisms with GO terms, EC numbers and KEGG pathways. The annotation is based on BLAST similarity searches against annotated subsets of EMBL UniProt from which sequences with non-informative entries have been removed. GO, EC and KEGG annotations are saved as flat files and in a relational postgreSQL database to allow for more sophisticated searches within the results.

::DEVELOPER

Ralf Schmid and Mark Blaxter

:: REQUIREMENTS

:: DOWNLOAD

annot8r

:: MORE INFORMATION

KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML

KEGG2SBML 1.5.0

:: DESCRIPTION

KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML’s capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.

::DEVELOPER

Akiya Jouraku, Nobuyuki Ohta and Akira Funahashi , Dept. of Biosciences and Informatics at Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

KEGG2SBML

:: MORE INFORMATION

Citations

  1. Converting KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).
  2. Converting the KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    5th International Conference on Systems Biology (ICSB 2004), October, 2004.

KEGG2SBML License