Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/46349

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
KeywordsBioinformatics
Biological system modeling
Biomembranes
Databases
Genomics
Organisms
Proteins
Bioinformatics
Genome Transporters Inference
Genome-scale metabolic models
Systems Biology
TRIAGE
Transport Reactions
merlin
Issue date2017
PublisherIEEE
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.
TypeArticle
URIhttp://hdl.handle.net/1822/46349
DOI10.1109/TCBB.2016.2527647
ISSN15455963
e-ISSN1557-9964
Publisher versionhttp://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=8857
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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