Empower Protein and Antibody Expression By GenSmart Codon Optimization

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Empower Protein and Antibody Expression By GenSmart Codon Optimization

In this webinar, Senior Manager of GenScript Bioinformatics R&D Department, Dr. Leo Fan, gave a review of the knowledge of GenSmart Codon Optimization algorithm and introduced what are the factors associated with DNA expression. Last but not the least, Dr. Fan provided a solution that improve protein expression at DNA level with GenSmart Codon Optimization Tool.

It has been well known that there are over hundreds of factors affecting protein expression. So is it possible to identify which factor is the most important or if we can rank these factors? In fact, it is hard for the scientists to rank these factors since the process of protein expression is extremely complicated when one codon changes, the values of a group of factors change simultaneously. Thus, all of the factors are not completely independent. And it is hard for us to evaluate their effects from a single side.

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the causes and consequences of codon bias

In the talk, Dr. Fan also explained that it’s a different story to mRNA and Protein. We may find some factors only have a significant effect on mRNA level or protein level with statistical significance, but some factors could influence both levels. It is demonstrated that various parameters have different stories and play different roles. So it is not easy to conclude it is significant or not.

So what’s the algorithm for GenSmart Codon Optimization Tool? The principle is to draw on the advantages and avoid disadvantages. The algorithm of GenSmart can be computed into 3 steps

Step 1. Collecte the highly expressed genes and perform the data mining to characterize high expression features such as codon frequency and codon pair frequency.

Step 2. Utilize the genetic algorithm to optimize three objective functions including the harmony index, codon context index and outlier index.

Step 3. Remove the adverse motifs. The adverse motifs were collected from publications or could be customized by users themselves. The backend genetic algorithm (GA) is inspired by the process of natural selection and it belongs to the evolutionary algorithms (EA).

algorithm for GenSmart Codon Optimization Tool

Up to date, GenScript GenSmart Codon Optimization tool has been applied to 50 host organisms, including the CHO, Human, T cell, E. coli, Insect and other commonly used species. It is a free and user-friendly tool for our customers. GenScript aims to help you get more active protein for your further study with the help of GenSmart Codon Optimization tool. In addition, you can order the optimized sequences through GenSmart Instant Quote System which has been seamless integrated with GenSmart Codon Optimization tool.

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Discuss on GenSmart Codon Optimization Tool

What are the advantages of the GenSmart codon optimization algorithms

It is demonstrated by other researchers from different fields that GenSmart codon optimization algorithms could boost higher protein expression and decrease immunogenicity.
How do you come up with applying the Population Immune Algorithm to codon optimization algorithm

Immune Algorithm could increase the diversity of population and avoid population degradation. So it is beneficial to improve the capability to get the optimal individual.
Would you like to further explain a bit why you identified these factors for the GenSmart codon optimization algorithms

We have done a lot of experiment to validate and identify these suitable parameters.
I want to optimize for other species outside of these fifty species, can the GenSmart codon optimization algorithm support it? Do I need to provide any additional information

Yes, we need species name and these species should have a well-annotated genome.
What do you think the next step in the development of codon optimization algorithms

Generate mutation library and get the expression data, and then use AI method to do data mining. But whether we could achieve better improvement, it is uncertain. And it will cost too much.