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AUTOGRAPH specifications


Unique identifier OMICS_20092
Alternative name AUtomatic Transfer by Orthology of Gene Reaction Associations for Pathway Heuristics
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Maintained Yes


No version available


  • person_outline Richard A Notebaart
  • person_outline Frank HJ van Enckevort
  • person_outline Christof Francke

Publication for AUtomatic Transfer by Orthology of Gene Reaction Associations for Pathway Heuristics

AUTOGRAPH citations


A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

Microb Cell Fact
PMCID: 4672519
PMID: 26643044
DOI: 10.1186/s12934-015-0370-x

[…] S. thermophilus C106 and L. rhamnosus yoba 2012 have been created based on the NCBI reference sequences NC_013198.1 and NC_006448.1, respectively, using FiJo: in-house developed software based on the Autograph method [] using L. plantarum WCFS1 and S. thermophilus LMG18311 as reference models. Non-gene associated reactions from L. plantarum and S. thermophilus were added to the models of L. rhamno […]


Computational Approaches for Microalgal Biofuel Optimization: A Review

Biomed Res Int
PMCID: 4189764
PMID: 25309916
DOI: 10.1155/2014/649453

[…] ensive. Therefore, automation of the process has been of interest. A limited number of software tools for automated reconstruction are currently available (some examples are given in ); for instance, AUTOGRAPH [], GEMSiRV [], MicrobesFlux [], MetRxn [], Model SEED [, ], SuBliMinaL Toolbox [], FAME [], and RAVEN Toolbox [] can be named. A systematic comparison between some of these platforms can be […]


Zea mays iRS1563: A Comprehensive Genome Scale Metabolic Reconstruction of Maize Metabolism

PLoS One
PMCID: 3131064
PMID: 21755001
DOI: 10.1371/journal.pone.0021784

[…] nome-scale model of A. thaliana to be used as a proxy. Using these GPRs as a point of comparison we next identified Arabidopsis gene orthologs in maize and transferred the corresponding GPRs via the AUTOGRAPH method . This step was followed by annotation of the remainder maize genes by bidirectional protein BLAST (i.e., BLASTp) searches against the NCBI non-redundant (nr) database. Out of a total […]


Genome scale models of bacterial metabolism: reconstruction and applications

FEMS Microbiol Rev
PMCID: 2704943
PMID: 19067749
DOI: 10.1111/j.1574-6976.2008.00146.x

[…] m ()] provided by some metabolic databases. Orthology relationships are sought between reference sequences from these databases and the coding sequences from the new genome. While these methods [e.g. autograph (), or identics (), see ] simplify the reconstruction process, they usually do not benefit from advanced annotation techniques, such as those derived from structural genomics or domains reco […]


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AUTOGRAPH institution(s)
Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Nijmegen, Netherlands; NIZO food research BV, Ede, Netherlands; Wageningen Center for Food Sciences, Wageningen, Netherlands
AUTOGRAPH funding source(s)
Supported by a BSIK grant through The Netherlands Genomics Initiative (NGI) and (ii) The Kluyver Centre for Genomics of Industrial Fermentation.


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