Publications in International Journals / Series (Article (International))

Genome-wide semi-automated annotation of transporter systems

  • IEEE-ACM Transactions on Computational Biology and Bioinformatics, 14(2), 443-456, 2017

Publisher: IEEE

Abstract

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 o ...

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