Gene synthesis design: a pythonic approach
Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. Ho...
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| Published in | PeerJ (San Francisco, CA) Vol. 12; p. e17750 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
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PeerJ. Ltd
26.07.2024
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| Online Access | Get full text |
| ISSN | 2167-8359 2167-8359 |
| DOI | 10.7717/peerj.17750 |
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| Abstract | Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function. |
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| AbstractList | Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function. Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function.Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function. |
| ArticleNumber | e17750 |
| Audience | Academic |
| Author | Pan, Danni Hu, Yunzhuo Chen, Xuanyang Xu, Fei Huang, Bifang Lin, Shiqiang |
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| Cites_doi | 10.1016/j.tibtech.2021.09.005 10.1016/0378-1119(95)00511-4 10.1093/nar/gki614 10.1186/1471-2105-7-285 10.1093/nar/gnh094 10.1093/protein/5.8.827 10.1093/nar/gki380 10.1093/nar/30.10.e43 10.1093/nar/gkh401 10.1038/s41587-022-01618-2 10.1093/nar/gkq143 10.1017/S0033583519000131 10.2174/1389203718666161117114243 10.1093/bioinformatics/btp163 10.1109/MCSE.2007.55 |
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| Keywords | DNA fragment Gene synthesis PCR Python |
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| SubjectTerms | Algorithms Anopheles Biochemistry Bioinformatics Biotechnology DNA - genetics DNA fragment Gene synthesis Genes Genes, Synthetic - genetics Molecular Biology Organic compounds PCR Polymerase Chain Reaction - methods Programming Languages Python Software Synthesis Synthetic Biology - methods |
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| Title | Gene synthesis design: a pythonic approach |
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