:: DESCRIPTION
KEGGParser is a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
MIDAS is an algorithm that determines condition specific subpaths, each of which has different activities across multiple phenotypes. MIDAS utilizes gene expression quantity information fully and the network centrality information to determine condition specific subpaths.
::DEVELOPER
Bio & Health Informatics Lab , Seoul National University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lee S, Park Y, Kim S.
MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data.
Methods. 2017 Jul 15;124:13-24. doi: 10.1016/j.ymeth.2017.05.026. Epub 2017 Jun 1. PMID: 28579402.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
KEGGscape is a pathway data integration and visualization app for Cytoscape.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
This application is released under the GPL v3 License: View License
Citation:
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
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.
:: 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
:: MORE INFORMATION
:: 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
:: MORE INFORMATION
Citations