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TitleGenome-wide semi-automated annotation of transporter systems
Author(s)Dias, Oscar
Gomes, Daniel G.
Vilaça, P.
Cardoso, João
Rocha, Miguel
Ferreira, Eugénio C.
Rocha, Isabel
Biological system modeling
Genome Transporters Inference
Genome-scale metabolic models
Systems Biology
Transport Reactions
Issue date2017
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
CitationDias, Oscar; Gomes, Daniel G.; Vilaça, P.; Cardoso, João; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel, Genome-wide semi-automated annotation of transporter systems. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 14(2), 443-456, 2017
Abstract(s)Usually, transport reactions are added to genome-scale metabolic models (GSMMs) based on experimental data and literature. This approach does not allow associating specific genes with transport reactions, which impairs the ability of the model to predict effects of gene deletions. Novel methods for systematic genome-wide transporter functional annotation and their integration into GSMMs are therefore necessary. In this work, an automatic system to detect and classify all potential membrane transport proteins for a given genome and integrate the related reactions into GSMMs is proposed, based on the identification and classification of genes that encode transmembrane proteins. The Transport Reactions Annotation and Generation (TRIAGE) tool identifies the metabolites transported by each transmembrane protein and its transporter family. The localization of the carriers is also predicted and, consequently, their action is confined to a given membrane. The integration of the data provided by TRIAGE with highly curated models allowed the identification of new transport reactions. TRIAGE is included in the new release of merlin, a software tool previously developed by the authors, which expedites the GSMM reconstruction processes.
Publisher version
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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