Method selection page

Select a method of calculating adherence to codon usage bias.

Click here for short descriptions of the methods (and links to articles describing them)

Organism: Bacillus endophyticus


Methods that isolate translational efficiency bias

A Genetic Optimization Approach for Isolating Translational Efficiency Bias  [Raiford et al.]

Modified Self-Consistent Codon Index (mSCCI)  [Raiford et al.]

Frequency of Preferred Codons (FOP) [Ikemura]

Codon Adaptation Index (CAI) [ Sharp & Li]

Transfer RNA Adaptation Index (tAI) [dos Reis et al.]

Measure Independent of Length and Composition(MILC) Expression Level Predictor (MELP) [Supek and Vlahoviček]


Methods that isolate dominant bias

Major Codon Usage (MCU) [Kanaya et al.]

Self-Consistent Codon Index (SCCI) [Carbone et al.]


Methods that strictly measure level of bias

Effective Number of Codons (Nc) [Wright]

Scaled Chi Squared (Χ2) [Shields et al.]


Non-bias detection data

tRNA Gene Data [Lowe & Eddy]