Arsen Arakelyan1, Lilit Nersisyan. 1. Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia. aarakelyan@sci.am
Abstract
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 http://www.mathworks.com/matlabcentral/fileexchange/37561.
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 http://www.mathworks.com/matlabcentral/fileexchange/37561.
Authors: Hans Binder; Henry Wirth; Arsen Arakelyan; Kathrin Lembcke; Evgeny S Tiys; Vladimir A Ivanisenko; Nikolay A Kolchanov; Alexey Kononikhin; Igor Popov; Evgeny N Nikolaev; Lyudmila Pastushkova; Irina M Larina Journal: BMC Genomics Date: 2014-12-19 Impact factor: 3.969