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JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
2005
Nucleic Acids Research
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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]
2021
bioRxiv
pre-print
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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
2014
Frontiers in Bioengineering and Biotechnology
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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
2017
BMC Bioinformatics
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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
2011
BMC Bioinformatics
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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
2011
Biotechnology Journal
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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
2012
BMC Systems Biology
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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
2021
Biology
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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
2019
International Journal of Cancer Management
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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]
2021
bioRxiv
pre-print
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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
2010
Applied and Environmental Microbiology
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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
2008
Biology Direct
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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
2020
PeerJ
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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
2016
Biotechnology and Bioengineering
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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
2020
NAR Genomics and Bioinformatics
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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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