Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 8, Pages 3899-3910Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv294
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Funding
- PhD grant [SFRH /BD/47307/2008]
- ERDF-European Regional Development Fund through the COMPETE Programme
- National Funds through the FCT [FCOMP-01-0124-FEDER-009707, FCOMP-01-0124-FEDER-015079]
- FCT Strategic Project [PEst-OE/EQB/LA0023/2013]
- Project 'BioInd-Biotechnology and Bioengineering for improved Industrial and Agro-Food processes' [NORTE-07-0124-FEDER-000028]
- Project 'PEM-Metabolic Engineering Platform' [23060]
- Programa Operacional Regional do Norte, QREN, FEDER [2-O Novo Norte]
- Centre of Biological Engineering
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The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.
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