Related Experiment Video
Updated: Apr 26, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
21.2K
KEGGParser: parsing and editing KEGG pathway maps in Matlab
Arsen Arakelyan1, Lilit Nersisyan
1Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia. aarakelyan@sci.am
Bioinformatics (Oxford, England)
|January 8, 2013
Summary
KEGGParser is a new MATLAB tool that aids in analyzing KEGG pathway maps. It allows for parsing, editing, and visualizing pathway data, improving the use of the KEGG pathway database.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database provides manually drawn pathway maps.
- KEGG Markup Language (KGML) files lack complete information for reproducing pathway events shown in static images.
- Existing KEGG pathway parsers and editors have limitations in processing KGML files.
Purpose of the Study:
- To introduce KEGGParser, a novel tool for the KEGG pathway database.
- To enable parsing, semiautomatic fixing, editing, visualization, and analysis of KEGG pathways within the MATLAB environment.
- To provide a solution for overcoming limitations in KGML file processing.
Main Methods:
- Development of KEGGParser as a MATLAB-based tool.
- Implementation of functionalities for parsing KGML files.
- Integration of editing, visualization, and analysis capabilities within MATLAB.
- Ensuring compatibility with Scilab for broader accessibility.
Main Results:
- KEGGParser facilitates the analysis of KEGG pathway data.
- The tool enables semiautomatic fixing and editing of pathway information.
- Visualization and analysis of pathway maps are enhanced within MATLAB.
- The software provides a more complete representation of pathway events.
Conclusions:
- KEGGParser offers a comprehensive solution for working with KEGG pathway data.
- The tool enhances the utility of the KEGG pathway database for researchers.
- KEGGParser supports both MATLAB and Scilab environments, promoting wider adoption.
Related Concept Videos
01:27C4 Pathway and CAM
37.9K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
C4 Pathway
The C4 pathway is used by plants such as...
37.9K
01:07MAPK Signaling Cascades
7.3K
Mitogen-activated protein kinase, or MAPK pathway, activates three sequential kinases to regulate cellular responses such as proliferation, differentiation, survival, and apoptosis. The canonical MAPK pathway starts with a mitogen or growth factor binding to an RTK. The activated RTKs stimulate Ras, which recruits Raf or MAP3 Kinase (MAPKKK), the first kinase of the MAPK signaling cascade. Raf further phosphorylates and activates MEK or MAP2 Kinases (MAPKK), which in turn phosphorylates MAP...
7.3K
01:24Introduction to MATLAB
1.2K
MATLAB stands for Matrix Laboratory. MathWorks developed MATLAB as a multi-paradigm numerical computing environment and proprietary programming language. It has evolved significantly over the years to become a tool utilized by engineers, scientists, and mathematicians for various tasks, including matrix calculations, developing algorithms, data analysis, and visualization. MATLAB's applications span various industries and disciplines. It's used in image and signal processing,...
1.2K