Gene design for heterologous expression.

Odysseus is a software for the design of typical protein-coding sequences for heterologous expression applications in common model organisms. The software realizes a probabilistic approach based on Markov models, that is highly configurable and can be trained with genomic data sets to learn the specific characteristics of common expression systems, such as S. cerevisiae, E. coli, A. thaliana or other.

For the profile generation, besides whole genome data sets also reduced subsets can be used, that are for instance restricted to low or high abundant proteins or protein classes with specific functional roles. Based on these trained profiles, the gene design software enables the user to generate a set of synonymous CDS sequences, for a given gene or protein sequence, all with the same level of typicity with respect to the preset profile.

Typical genes showed to be well suited for the controlled regulation of the heterologous expression of proteins in such a way that a controlled decrease or increase in the rate of expression can be achieved. For detailed information with insights into an examplary expression study of GFP and human alpha-synuclein (AD) in yeast (S. cerevisiae), see our new publication referenced below or the Documentation and FAQs.

Software Features:

Profiles

Choose out of pre-trained profiles for common model organisms.

Customize profiles dynamically by protein classes, functions or abundance (PaxDB).

Filtering and Exclusion

Recognition and cleavage sites of restriction enzymes (site-types, commercial usage from REBASE).

Stability levels predicted by RNAFold (ViennaRNA).

Regulate expression levels

Optimize the amounts of synthesized protein products e.g. for biopharmaceutical applications.

Avoid toxic effects by overexpressing proteins in expression systems.

1. Step: Input information

Paste the sequence information of the protein or gene of your interest in the input mask.

Choose the number of modified sequences to be generated.

Select a pre-trained profile for the adaptation to a model organism and press Generate.

2. Step: Detailed configuration (optional)

Filter resulting synonymous gene sequences for certain restriction sites or RNA stability levels (MFE).

Dynamically create a custom profile with alternative codon-usage weighting or by restricting the host genome data to protein subsets with specified abundancies or functional classes.

3. Step: Inspect generated synonymous gene sequences

Compare DNA sequence suggestions by functional alignments (plain, amino acids, codon differences).

Inspect single gene information such as sequence statistics, RNA stability and structure or base pairing sites.

Control the profile information of the model and the suggested genes (codon-usage heatmaps and tables).

Using Odysseus by non-academics requires permission. Odysseus may be obtained upon request and used under a Creative Commons BY-NC-SA 4.0 International License.