ChimeraUGEM WebGUI

The ChimeraUGEM WebGUI is a bioinformatics tool for the analysis of gene sequences (coding and non-coding), as well as the design of protein coding sequences for optimized expression. It differs from other tools in that it:

• Can capture long host-specific regulatory patterns that may be missed by simple codon optimization
• Does not require expression data (unsupervised): For example, in a recent study we show that ChimeraARS scores predict heterologous expression levels in a plant-based system, where little data is available for training of ML models.
• Allows for the design of multiple optimized variants for the target protein with minimal homology to ensure genetic stability in multi-copy systems

1. Provide proteins to optimize or nt sequences to analyze
2. Select or upload a set of reference sequences, typically coding sequences from the host organism of interest. For convenience, coding sequences for several model organisms are provided from their NCBI reference genomes.
3. Set parameters, reasonable default values are provided. Check the tooltips for information about each parameter.
4. Results are provided as FASTA (optimized sequences) or CSV (ChimeraARS scores) files