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I am reaching the end of my PhD on algal molecular biology and have found the CUO extremely useful. To date my use of it has fallen into three categories. My initial use of it was for the assisted design or redesign of several recombinant genes for expression in the Chlamydomonas reinhardtii chloroplast, a task which it has excelled at. Further to this I have used the program extensively for the analysis of previously expressed genes in the C. reinhardtii chloroplast to evaluate trends in expressing and non-expressing sub-sets. The CUO has also proven to be a very powerful tool for the study of the codon and codon pair usage in genes native to the C. reinhardtii chloroplast, a task I would have been unable to complete without this program.
Team:UCLondon/testing-bay/test1
From 2012e.igem.org
Morph
Bioinformatics
Codon Usage Optimizer
Advancing Protein Expression
Codon Usage Optimizer (CUO) is a GUI-based multiplatform software written in Java. The main function of the software is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome using an original set of algorithms for calculation, data processing and automated reasoning. Furthermore, it can be used as an electronic drawboard for gene sequence analysis and design. While the software focuses on the C.reinhardtii genome, it can also be used to optimize genes into other hosts as well. Since E.coli and S.cerevisiae are popular candidates of biotechnological exploitation, they will be CUO's next shift of focus in its development.
| Elevator Pitch |
Tutorials |
Slide Deck |
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| In the elevator pitch we describe the unique selling point of CUO and detail our plans on how we will commercialize it using the open source platform. | These tutorials demonstrate key features of CUO and help new users unleash its the awesome power. | In the slide deck we describe the unique selling point of CUO and detail our plans on how we will commercialize it using the open source platform |
Draft Pitch |
Tutorials |
Get the latest version of CUO!
Download
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Last Modified: 14.10.2012 |
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Kasuza Table parser added |
release notes |
 CUO beta0.92 released!I am delighted to announce the release of CUO beta0.92! This release humbly marks the new era of CUO. The team had grown and sprouted like never before. With the recent recruitment of four professional bioinformaticians and a web developer into the dev team, the program is entering an accelerated development phase that was previously impossible. We even have a public engagement officer on board now to make the software more interactive from all aspects (check out our social networks :D ). Many thanks again to all the people supporting, building and using CUO. The result presented here is an accumulation of efforts and help from everyone. Featuring:
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Testimonials
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I have used CUO to optimize several gene and tag sequences for expression in the Chlamydomonas chloroplast. The advantage of this program lies in its integration of codon usage with codon pairing optimization, using data from highly expressed genes. The interface is professional, flexible and easy to navigate and the manual provides clear instructions. Whilst we are still gathering data, early indications are that the program performs very well in redesigning genes for optimal expression.
