Fitness Functions
This section details the objective functions available for the genetic algorithm (GA). Each fitness module evaluates a specific biological or biophysical property of the query sequence, returning a numerical score that drives the optimization landscape.
Overview
The optimization engine accepts a list of fitness objects. During the evolutionary process, these metrics are computed to rank candidate sequences.
Common Parameters: Every fitness function accepts the following optional parameter:
| Parameter | Type | Default | Description |
|---|---|---|---|
weight |
float |
1.0 |
Determines the magnitude and direction of the fitness vector. Positive values maximize the metric; negative values minimize it. |
Fitness list
1. RNA Pseudoyield
Description A metric based on deep learning predicting the yield of in vitro RNA transcription (IVT). It calculates a measure of IVT yield of full-length RNA molecules.
Arguments
* weight (float, optional): Optimization weight.
2. Manufacturability
Description A metric that takes into account rules for RNA manufacturability such as GC content and codon usage.
Arguments
* weight (float, optional): Optimization weight.
3. CAI (Codon Adaptation Index)
Description Quantifies the conformity of the sequence's codon usage to the synonymous codon usage bias of a reference set of highly expressed genes. High CAI values are theoretically linked to efficient translation elongation and reduced metabolic burden.
Arguments
* weight (float, optional): Optimization weight.
4. U% (Uridine Content)
Description Calculates the percentage of uridine nucleotides within the sequence. In the context of mRNA therapeutics, reducing U-content (U-depletion) is a strategy to minimize immunogenicity via Toll-like receptor (TLR) evasion and to improve mRNA stability.
Arguments
* weight (float, optional): Optimization weight.
Technical Summary
| ID | Name | Range |
|---|---|---|
| ppy | RNA Pseudoyield | Unbounded |
| rna_manufact | RNA Manufacturability | (0, 1] |
| cai | Codon Adaptation Index | (0, 1] |
| u_perc | Uridine Percentage | (0, 1] |