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JCat: a novel tool to adapt codon usage of a target gene to its potential expression host

A. Grote, K. Hiller, M. Scheer, R. Munch, B. Nortemann, D. C. Hempel, D. Jahn
2005 Nucleic Acids Research  
A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production.  ...  In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method.  ...  Funding to pay the Open Access publication charges for this article was provided by BMBF. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gki376 pmid:15980527 pmcid:PMC1160137 fatcat:cxp6sflruvbkhnmmwmm2j7jsue

Designing a Novel Multi-Epitope Vaccine against SARS-CoV-2; Implication for Viral Binds and Fusion Inhibition through Inducing Neutralizing Antibodies [article]

Seyed Amir Hossein Mohammadzadeh Hosseini Moghri, Mojtaba Ranjbar, Hadi Hassannia, Fatemeh Khakdan
2021 bioRxiv   pre-print
Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to public health so it is an emergency to vaccine development.  ...  In the present study, several immunoinformatics tools are used for analyzing the spike (S) glycoprotein sequence including the prediction of the potential linear B-cell epitopes, B-cell multi-epitope design  ...  JCat: a novel tool to adapt 367 codon usage of a target gene to its potential expression host. Nucleic acids research, 33(suppl_2), pp.W526-W531. 27 . 27 Morla, S., Makhija, A. and Kumar, S., 2016.  ... 
doi:10.1101/2021.06.16.448772 fatcat:73pe4j4lmrfr7ffxleq5fdfnhm

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Nathan Gould, Oliver Hendy, Dimitris Papamichail
2014 Frontiers in Bioengineering and Biotechnology  
The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation.  ...  To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties  ...  ACKNOWLEDGMENTS We would like to thank the two reviewers for their constructive suggestions and comments.  ... 
doi:10.3389/fbioe.2014.00041 pmid:25340050 pmcid:PMC4186344 fatcat:fbqeuf2ewvcxhpdm7d3td7ueka

Novel methods to optimize gene and statistic test for evaluation – an application for Escherichia coli

Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
2017 BMC Bioinformatics  
However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down  ...  In addition, genes optimized by our methods seem to associate with highly expressed genes and give reasonable codon adaptation index values.  ...  Acknowledgements We would like to thank Dr. Nguyen Duc Hoang, Msc Funding Not applicable.  ... 
doi:10.1186/s12859-017-1517-z pmid:28187713 pmcid:PMC5303253 fatcat:3rvwf42rvbaodlchwxb42jnjve

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

Sang-Kyu Jung, Karen McDonald
2011 BMC Bioinformatics  
Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications.  ...  In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer.  ...  The development of Visual Gene Developer was partially funded by Chevron Technology Ventures (RSO #23). Authors' contributions SKJ conceived and developed the software.  ... 
doi:10.1186/1471-2105-12-340 pmid:21846353 pmcid:PMC3215308 fatcat:xhw745yagbg7fcsvjpzb3ciryi

Codon usage: Nature's roadmap to expression and folding of proteins

Evelina Angov
2011 Biotechnology Journal  
Thus, the focus of this review is to provide some experimental support and a brief overview of how codon usage bias has evolved relative to regulating gene expression levels.  ...  formation of a stable product.  ...  A third approach to recode a target gene sequence is to "match" the codon usage bias inherent in the native host more closely when expressed in the heterologous host and is referred to as "codon harmonization  ... 
doi:10.1002/biot.201000332 pmid:21567958 pmcid:PMC3166658 fatcat:5m4rya444jetdiao6jxcathyya

Computational codon optimization of synthetic gene for protein expression

Bevan Chung, Dong-Yup Lee
2012 BMC Systems Biology  
By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or  ...  Conclusions: The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine  ...  Acknowledgements This work was supported by the National University of Singapore, Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore and a grant from the Next-Generation  ... 
doi:10.1186/1752-0509-6-134 pmid:23083100 pmcid:PMC3495653 fatcat:icp2ykmycreyhdg4t7skoiwy44

Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches

Sidra Aslam, Sajjad Ahmad, Fatima Noor, Usman Ali Ashfaq, Farah Shahid, Abdur Rehman, Muhammad Tahir ul Qamar, Eid A. Alatawi, Fahad M. Alshabrmi, Khaled S. Allemailem
2021 Biology  
The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy.  ...  A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins.  ...  Acknowledgments: The researchers would like to thank the Deanship of Scientific Research, Qassim University for funding the publication of this project.  ... 
doi:10.3390/biology10100997 pmid:34681096 fatcat:mlflnwql7fbstldw2ndj7couoi

In Silico Evaluation of Two Targeted Chimeric Proteins Based on Bacterial Toxins for Breast Cancer Therapy

Zoleikha Goleij, Hamideh Mahmoodzadeh Hosseini, Mohsen Amin, Jafar Amani, Elham Behzadi, Abbas Ali Imani Fooladi
2019 International Journal of Cancer Management  
Results: The results of this study showed that codon adaptation index of s1 and p2 fusion gene has improved to 0.98 and .99, respectively.  ...  Therefore, HER2 can be a potential therapeutic target. To enhance the potency of HER2 blockers, the conjugation of specific cytotoxic agents with these types of anticancer agents may be successful.  ...  Codon usage was checked by java codon optimization tool (JCat) (http://www.jcat.de/), optimizer web server (23, 24) , and gene script server (http://www.genscript.com/).  ... 
doi:10.5812/ijcm.83315 fatcat:r3mqkhzfzzgxzkr5r7o7halxuq

The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes [article]

Astra S. Bryant, Elissa A. Hallem
2021 bioRxiv   pre-print
Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes.  ...  We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes.  ...  ., 2005 JCat: a novel tool 426 to adapt codon usage of a target gene to its potential expression host.  ... 
doi:10.1101/2021.02.18.431865 fatcat:ca5i4kdkwrchjoeq37prstdjdq

Application of the Saccharomyces cerevisiae FLP/FRT Recombination System in Filamentous Fungi for Marker Recycling and Construction of Knockout Strains Devoid of Heterologous Genes

K. Kopke, B. Hoff, U. Kuck
2010 Applied and Environmental Microbiology  
This cassette allows the controlled expression of the recombinase gene for one-step marker excision.  ...  As a proof of application of this system, we constructed a ⌬Pcku70 knockout strain devoid of any heterologous genes.  ...  Frankenberg-Dinkel for suggesting the use of JCat for codon adaptation, and Hubert Kürnsteiner, Ernst Friedlin, Ivo Zadra, Heiko Eichhorn, Rudolf Mitterbauer, and Thomas Specht (Sandoz GmbH) for their  ... 
doi:10.1128/aem.00670-10 pmid:20472720 pmcid:PMC2901726 fatcat:t32q2fm5qzhs3abgntsoretvfi

CAIcal: A combined set of tools to assess codon usage adaptation

Pere Puigbò, Ignacio G Bravo, Santiago Garcia-Vallve
2008 Biology Direct  
Conclusion: The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.  ...  The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set.  ...  IGB is the recipient of a professorship supported by the Volkswagen Stiftung in the program Evolutionary Biology.  ... 
doi:10.1186/1745-6150-3-38 pmid:18796141 pmcid:PMC2553769 fatcat:uz5jbyic6rf7fc246exerdxy74

An immunoinformatics approach for the design of a multi-epitope subunit vaccine for urogenital schistosomiasis

Olugbenga S. Onile, Adeyinka I. Fadahunsi, Ameerah A. Adekunle, Bolaji F. Oyeyemi, Chiaka I. Anumudu
2020 PeerJ  
A 3D structure of the vaccine construct was predicted, followed by disulphide engineering for stability, codon adaptation and in silico cloning for proper expression and molecular protein–protein docking  ...  Consequently, a 493 amino acid multi-epitope vaccine construct of antigenicity probability of 0.91 was designed. This was predicted to be stable, non-allergenic in nature and safe for human use.  ...  Codon adaptation of the designed vaccine was done according to the usage of E. coli (strain K12) expression system using JCAT server and found the codon adaptive index to be 0.95 whereas, a score close  ... 
doi:10.7717/peerj.8795 pmid:33062404 pmcid:PMC7534685 fatcat:vpk4gyugtnc45iqdpbdjg2qmlu

Synthetic gene design-The rationale for codon optimization and implications for molecular pharming in plants

Gina R. Webster, Audrey Y.-H. Teh, Julian K.-C. Ma
2016 Biotechnology and Bioengineering  
Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons.  ...  However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the 'optimal' gene sequence  ...  Acknowledgements We would like to thank the generous financial support of the European Research Council, through its Future-Pharma Advanced Grant Award, and the Hotung Foundation.  ... 
doi:10.1002/bit.26183 pmid:27618314 fatcat:7pfgoymogjf2xp2pcdu3pkiqwe

Development of multiepitope subunit protein vaccines against Toxoplasma gondii using an immunoinformatics approach

Olugbenga S Onile, Glory J Ojo, Bolaji Fatai Oyeyemi, Gbenga O Agbowuro, Adeyinka I Fadahunsi
2020 NAR Genomics and Bioinformatics  
The potential of vaccine to likely revert to virulent strain is a major reason why it has not been found suitable for human use, hence the need for a vaccine that will induce T and B memory cells capable  ...  The adverse effect of this parasite includes a serious congenital disease in the developing fetus of pregnant women.  ...  submitted into the Java Codon Adaptation Tool (JCat) server (http://www.prodoric.de/JCat) for codon optimization and reverse translation in the host Escherichia coli strain K12.  ... 
doi:10.1093/nargab/lqaa048 pmid:33575600 pmcid:PMC7671309 fatcat:3nmooffeqnh3xd3rlozh5tqhbi
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