CodonMuSe is a method for inferring the strength of selection acting on nucleotide sequences. It detects the strength of selection acting on the translation efficiency of the sequence and the strength of selection acting on biosyntheic cost of that sequence.
Most amino acids are encoded by multiple synonymous codons. These codons are not equal. They cost different mount of resources to make and they have different numbers of cognate tRNAs floating about in the cell. Thus, different codons encoding the same amino acid have different biosynthetic costs and different translational efficiencies. CodonMuSe figures out how these two competing selective forces interact to shape the coding sequence of genes. It also considers background effects such as genome-wide mutation bias.
If you want to know whether your gene has been under selection be cheap, efficient or both, ask CodonMuSe! It takes less than a second.
You can download and install CodonMuSe here
If you use CodonMuSe in your work please cite both:
Seward EA and Kelly S (2016). Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biology 17:226
Seward EA and Kelly S (2018). Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria. Genome Biology 19:102
You can also read Emily’s excellent PhD thesis on the subject here
Seward EA (2017). The Evolutionary Impact of Resource Availability DPhil Thesis