An overview of pathway prediction tools for synthetic design of microbial chemical factories

Bashir Sajo Mienda; Mohd Shahir Shamsir; Bashir Sajo Mienda; Mohd Shahir Shamsir

doi:10.3934/bioeng.2015.1.1

AIMS Bioengineering

2015, Volume 2, Issue 1: 1-14. doi: 10.3934/bioeng.2015.1.1

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An overview of pathway prediction tools for synthetic design of microbial chemical factories

Bioinformatics Research Group (BIRG), Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor. Malaysia

Received: 16 January 2015 Accepted: 10 February 2015 Published: 15 February 2015

The increasing need for the bio-based industrial production of compounds via microbial cell factories leads to a demand for computational pathway prediction tools. A variety of algorithms have been developed that can be used to identify possible metabolic pathways and their corresponding enzymatic parts. These prediction tools play a central role in metabolic pathway design and microbial chassis selection for industrial chemical production. Here, we briefly discuss how the development of some key computational tools, which are currently available for pathway construction, could facilitate the synthetic redesign of microbial chassis. Special emphasis is given to the characteristics and drawback(s) of some of the computational tools used in pathway prediction, and a generalized workflow for the design of microbial chemical factories is provided. Perspectives, challenges and future trends are briefly highlighted.
- metabolic pathways,
- computational tools,
- synthetic design,
- microbial chemical factories
Citation: Bashir Sajo Mienda, Mohd Shahir Shamsir. An overview of pathway prediction tools for synthetic design of microbial chemical factories[J]. AIMS Bioengineering, 2015, 2(1): 1-14. doi: 10.3934/bioeng.2015.1.1

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Abstract

The increasing need for the bio-based industrial production of compounds via microbial cell factories leads to a demand for computational pathway prediction tools. A variety of algorithms have been developed that can be used to identify possible metabolic pathways and their corresponding enzymatic parts. These prediction tools play a central role in metabolic pathway design and microbial chassis selection for industrial chemical production. Here, we briefly discuss how the development of some key computational tools, which are currently available for pathway construction, could facilitate the synthetic redesign of microbial chassis. Special emphasis is given to the characteristics and drawback(s) of some of the computational tools used in pathway prediction, and a generalized workflow for the design of microbial chemical factories is provided. Perspectives, challenges and future trends are briefly highlighted.

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