Enzyme2 is a command line tool to process and evaluate metabolic networks and microarray data. It uses the Affymetrix (Microarray), BioCyc (Pathway/Genome) and GO (Ontology) databases.
There are a number of relevant tools that can be used in combination with enzyme2 for metabolic networks and microarray data analysis : Bioconductor, Cytoscape, Galaxy, Mayday, MeV or Vanted.
For command documentation, start the program for the first time. enzyme2.macro is created with a complete list of commands.
This program is owned by Heiko Stark. It can be used free of charge for non-commercial use. For the common citations in publications, please use the following entry “Enzyme2 software (Heiko Stark, Jena, Germany, URL: https://starkrats.de)”.
An installer for Windows and Linux can be found here: Software
enzyme2 64bit (Windows & Wine/Darwine)
enzyme2 32bit (Windows, ReactOS & Wine/Darwine)
enzyme2 64bit (MacOS X & Darling)
enzyme2 32bit (MacOS X & Darling)
enzyme2 64bit (Linux)
enzyme2 32bit (Linux)
enzyme2 arm (Linux)
enzyme2 64bit (FreeBSD)
enzyme2 32bit (FreeBSD)
enzyme2 64bit (Solaris)
enzyme2 32bit (Solaris)
Note: Intel 32bit runs also on 64bit systems, but only with 4 GB memory!
▸ Build database example
//!enzyme2 // This is a comment for the enzyme macro - you can use this macro like a programing language // For more infos, please see https://stark-jena.de | enzyme // Copyright (c) 2011-201 by Heiko Stark load.metacycle "reactions.dat" load.metacycle.compound "compounds.dat" load.metacycle.enzyme "enzrxns.dat" // fill up enzyme names load.metacycle.gene "genes.dat" // fill up gene names load.metacycle.pathway "pathways.dat" // fill up pathway names print "How many organisms? : " organism.size // only if you use more than one organism print "How many metabolites? : " metabolite.size print "How many reactions? : " reaction.size print "How many enzymes? : " reaction.enzyme.size // only if you load additional enzymes (load.metacycle.enzyme) print "How many reaction genes? : " reaction.gene.size // only if you load additional genes (load.metacycle.gene) print "How many genes? : " regulator.gene.size // only if you load additional genes (load.metacycle.gene) print "How many pathways? : " reaction.pathway.size // only if you load additional pathways (load.metacycle.pathway) load.ontology "gene_ontology_ext.obo" load.kegg "mmu.list" annotation.clear database.save "database.fast" // full database
▸ Show database example
//!enzyme2 // This is a comment for the enzyme macro - you can use this macro like a programing language // For more infos, please see https://stark-jena.de | enzyme // Copyright (c) 2011-2015 by Heiko Stark // Show statistics metabolite.clearname := true // false S###S | true metabolite metabolite.withlocation := true // false metabolite | true metabolite[?] ifexists "database.fast" then load.database "database.fast" end else print "No database found!" stop end print "How many organisms? : " organism.size // only if you use more than one organism print "How many metabolites? : " metabolite.size print "How many reactions? : " reaction.size io.dir.hardchange "Complete" pathway.complete print "Reactions: " pathway.size pathway.save "pathway.list" index pathway.save "pathway.eclist" ec pathway.save "pathway.namelist" name pathway.savepathways "pathways.name" sortname pathway.savepathways "pathways.count" sortcount pathway.savepathways "pathways.index" sortindex pathway.savepathways "pathways.group" group pathway.saveignore "pathwayignore.eclist" ec pathway.savemetaused "pathwaymetaused.list" index pathway.savemetaused "pathwaymetaused.namelist" name pathway.savemetacount "pathwaymetacount.list" index pathway.savemetacount "pathwaymetacount.namelist" name metabolite.clearname := false pathway.savemetatool "pathway.dat" index auto metabolite.clearname := true pathway.savemetatool "pathway.ecdat" ec auto pathway.savegml "pathway.gml" 18 metabolite.clearname := false reaction.save "reaction.idlist" index metabolite.clearname := true reaction.save "reaction.eclist" ec reaction.save "reaction.list" index // metabolite.sort // after sorting the metabolite the reaction is empty metabolite.save "metabolite.list" index
Used for the Gerontoshield project.
And used for these investigations:
Fichtner M, Schuster S & Stark H (2020) Determination of scoring functions for protein damage susceptibility. Biosystems 187: 104035. DOI:10.1016/J.BIOSYSTEMS.2019.104035 / ISSN:0303-2647
If you want to send me a bug report or have some suggestions about what future versions of ‘enzyme2’ should support, you can contact me either by email (bugs[@]starkrats[dot]de).