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Estimates of codon optimization can be used to identify genes that are expressed at high levels and are important for organismal ecology. Here, we will use the metric gRSCU (gene-wise relative synonymous codon usage), which is a function in the bioinformatic toolkit BioKIT, to estimate codon optimization.
gRSCU is calculated by determining the mean or median relative synonymous codon usage value for all codons in each gene based on their genome-wide values.
If you found BioKIT useful, please cite BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Steenwyk et al. 2022, GENETICS. doi: 10.1093/genetics/iyac079.