The uploaded sequence uses the extended IUPAC sequence alphabet (with additional ambiguous aminoacids [B,X,Z,J,U,O]), which leads to problems in the generation of the synonymous DNA sequences. Please change your uploaded sequence into a compatible format.
Gene design for heterologous expression.
A software to support controlled protein biosynthesis regulation in modern expression systems.
Designing typical genes with Odysseus
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.
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.
If Odysseus is helpful for your research, please cite:
Simm D., Popova B., Braus G. H., Waack S. and Kollmar M. (2021) Design of typical genes for heterologous gene expression.
Scientific Reports. 12(9625). - 10.1038/s41598-022-13089-1
Quick Start Guide
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.