An overview of pathway prediction tools for synthetic design of microbial chemical factories
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 p...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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AIMS Press
2015-02-01
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| Series: | AIMS Bioengineering |
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| Online Access: | http://www.aimspress.com/Bioengineering/article/160/fulltext.html |
| _version_ | 1818258079555256320 |
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| author | Bashir Sajo Mienda Mohd Shahir Shamsir |
| author_facet | Bashir Sajo Mienda Mohd Shahir Shamsir |
| author_sort | Bashir Sajo Mienda |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T17:53:51Z |
| format | Article |
| id | doaj.art-4bf7bb502a2747559960cbee59b5503a |
| institution | Directory Open Access Journal |
| issn | 2375-1495 |
| language | English |
| last_indexed | 2024-12-12T17:53:51Z |
| publishDate | 2015-02-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Bioengineering |
| spelling | doaj.art-4bf7bb502a2747559960cbee59b5503a2022-12-22T00:16:45ZengAIMS PressAIMS Bioengineering2375-14952015-02-012111410.3934/bioeng.2015.1.120150101An overview of pathway prediction tools for synthetic design of microbial chemical factoriesBashir Sajo Mienda0Mohd Shahir Shamsir1Bioinformatics Research Group (BIRG), Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor. MalaysiaBioinformatics Research Group (BIRG), Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor. MalaysiaThe 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.http://www.aimspress.com/Bioengineering/article/160/fulltext.htmlmetabolic pathwayscomputational toolssynthetic designmicrobial chemical factories |
| spellingShingle | Bashir Sajo Mienda Mohd Shahir Shamsir An overview of pathway prediction tools for synthetic design of microbial chemical factories AIMS Bioengineering metabolic pathways computational tools synthetic design microbial chemical factories |
| title | An overview of pathway prediction tools for synthetic design of microbial chemical factories |
| title_full | An overview of pathway prediction tools for synthetic design of microbial chemical factories |
| title_fullStr | An overview of pathway prediction tools for synthetic design of microbial chemical factories |
| title_full_unstemmed | An overview of pathway prediction tools for synthetic design of microbial chemical factories |
| title_short | An overview of pathway prediction tools for synthetic design of microbial chemical factories |
| title_sort | overview of pathway prediction tools for synthetic design of microbial chemical factories |
| topic | metabolic pathways computational tools synthetic design microbial chemical factories |
| url | http://www.aimspress.com/Bioengineering/article/160/fulltext.html |
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