DNA Optimization
Cluster Design

EvoMAG - ATG's expert tool for analyzing formal functional gene sequence features and for optimizing expression relevant sequence parameters.

Based on years of service to and feed-back from our customers and as a response to their specific requirements, ATG has continuously developed the EvoMAG - GeneIntelligence software to optimize constructive (overall design, synthesis efficiency) and functional (expression, solubility, etc.) aspects.

EvoMAG was designed to compute many relevant parameters in the gene optimization process in parallel. The gene sequence is subjected to a tournament situation where many variants compete for the best fit. Certain parameters can be given more weight than others and this will reflect in the output.

If you wish to improve the codon bias of your genes towards deploying a high expression table or production specific table but simultaneously you like to avoid extended sequence repeats, EvoMAG can preferentially calculate it away. EvoMAG will find the best compromise e.g. at minimal cost of suboptimal GC-content or distribution.

Relative adaptiveness

Codon usage

Restriction sites


Pareto graph

Local CAI

PolyN - stretches

Sequence repeats

Secondary structure

Slow codon clusters

Cryptic splice sites

Fig.1. Multi-Parameter Gene Sequence Optimization: In most cases it is not possible to achieve a high level of optimization for all relevant sequence features simultaneously. Instead, one is faced with a continuum of possibilities. These are largely determined by the given amino acid sequence (that is encoded within the gene sequence) and the codon usage in the target organism (that codon usage tables describe). In the animation shown above, forcing the CG-content into its desired limits for example can result in the formation of slow codon clusters. Correspondingly, the removal of extreme sequence repeats can lead to a higher probability for the presence of illegitimate donor splice sites. In fact, within the framework of optimization, nearly all sequence features or groups of sequence features may be considered more or less as interdependent variables. Similar to most other real-world multi-objective optimization problems, there is often no single "best solution", but rather a plurality of "best compromise" sequence variants. Of course, there are also "hard" disqualifiers, e.g. the presence of gene-toxic sequence motifs.

Modular Molecular Systems: Combining Synthetic Bioinformatics with GeneCluster Designs for Multi-Protein Expression and Minimal Molecular Function.
  • Based on years of service to and feed-back from our customers and as a response to their specific requirements, ATG has continuously developed the evoMAG - GeneIntelligence software for expression optimization.
  • EvoMAG stands for: in silico evolution-mediated artificial genetics.
  • Evolutionary genetic algorithms calculate multiple gene sequence parameters simultaneously in silico for diverse functional optimizations of formal-operational gene features.
  • Heterologous gene expression regularly requires adaption of codon usage and even homologous genes can be optimized for production and regulation by use of EvoMAG if needed.
  • Any gene and gene cassette cloned into our multi-gene assembly and expression systems can be adapted for optimal expression of the whole set of functionally related genes by systematically employing EvoMAG - algorithms.
  • To get a grip on the animated image to the left, we will soon offer a short tour through parameter country. It will help the non-expert understand what gene optimization is all about, how it works and what it can do for him.

Sequence Optimization: What we can do for you - parameters, genetic elements and solutions

If you opt for optimization, this is what we can do for you - either a:

A) standard (basic) optimization, or
B) an in-depth expert level (customer-specific) optimization that will address any specific detail you consider relevant.

Standard optimization: Covers only the coding region/ORF of a gene: translational elongation is formally optimized by adapting your sequence using custom tables for codon frequencies.

Expert optimization: We first analyze which additional parameters may become critical, make suggestions and then work out a specific solution together with you, the customer.

This is what expert level optimizations can look like:
  1. Level I: Gene Check
  2. Level II: Gene Check + Translation Elongation with modified tables
  3. Level III: Gene Check + Translation Elongation with modified tables + Translation Initiation
  4. Level IV: Gene Check + Translation Elongation with modified tables + Translation Initiation + Translation Termination
  5. Level V: like Level IV but for gene clusters