StAIcalc: TRNA adaptation index calculator based on species-specific weights

Abstract

The tRNA Adaptation Index (tAI) is a tRNA-centric measure of translation efficiency which includes weights that take into account the efficiencies of the different wobble interactions. To enable the calculation of the index based on a species-specific inference of these weights, we created the stAIcalc. The calculator includes optimized tAI weights for 100 species from the three domains of life along with a standalone software package that optimizes the weights for new organisms. The tAI with the optimized weights should enable performing large scale studies in disciplines such as molecular evolution, genomics, systems biology and synthetic biology.