KEGGParser: parsing and editing KEGG pathway maps in Matlab

Bioinformatics. 2013 Feb 15;29(4):518-9. doi: 10.1093/bioinformatics/bts730. Epub 2013 Jan 3.


Summary: KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab.

Availability and implementation: The source code is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Graphics
  • Databases, Factual
  • Metabolic Networks and Pathways
  • Signal Transduction*
  • Software*