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Database and Tools for Metabolic Network Analysis
Lu Shi Jing,Farah Fathiah Muzaffar Shah,Mohd Saberi Mohamad,Nur Laily Hamran,Abdul Hakim Mohamed Salleh,Safaai Deris,Hany Alashwal 한국생물공학회 2014 Biotechnology and Bioprocess Engineering Vol.19 No.4
Metabolic network analysis has attracted muchattention in the area of systems biology. It has a profoundrole in understanding the key features of organismmetabolic networks and has been successfully applied inseveral fields of systems biology, including in silico geneknockouts, production yield improvement using engineeredmicrobial strains, drug target identification, and phenotypeprediction. A variety of metabolic network databases andtools have been developed in order to assist research inthese fields. Databases that comprise biochemical data arenormally integrated with the use of metabolic networkanalysis tools in order to give a more comprehensive result. This paper reviews and compares eight databases as wellas twenty one recent tools. The aim of this review is tostudy the different types of tools in terms of the featuresand usability, as well as the databases in terms of the scopeand data provided. These tools can be categorised intothree main types: standalone tools; toolbox-based tools;and web-based tools. Furthermore, comparisons of thedatabases as well as the tools are also provided to helpsoftware developers and users gain a clearer insight and abetter understanding of metabolic network analysis. Additionally, this review also helps to provide usefulinformation that can be used as guidance in choosing toolsand databases for a particular research interest.
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