STADIUM: Species-specific Trna ADaptive Index compendiUM

About STADIUM

  As increasing interest on synonymous codon, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and calculated based on intracellular tRNA abundances and binding strength between a codon and a tRNA (evaluating the availability of tRNA corresponding to each codon rather than Codon itself). The index was widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, improved version of the index, names species-specific tAI (stAI), was developed by adapting tRNA copy numbers in species. Although a subsequenctly developed webserver (stAIcalc) provides tools that calculated stAI values, it was not available to access pre-calculated values. In addition to about 100 species in the stAIcalc, we calculated stAI values for whole coding sequences in 148 species. To enable easy access to this index, we constructed a novel web database, named STADIUM (Species-specific tRNA adaptive index compendium). STADIUM provides not only stAI value of each gene, but also provides statistics based on pathway-based classification. The database is expected to help researchers who have interests of codon optimality and role of synonymous codon.



Citation

STADIUM: Species-specific tRNA adaptive index compendium
Jonghwan Yoon, Yeun-Jun Chung∗, and Minho Lee∗
2018, Genomics & Informatics, 12(4)

The tAI for each gene.

This table contains the names of the input genes and their resultant tAI values based on the species-specific inferred weights.

The weights for each codon.
Pathways of selected species.
Summary of pathway for each species
Species of selected pathway

Download

Whole tAI values are available for download here : Raw_tAI.csv

The codon weight values are available for download here : Raw_codon_weights.csv

Contact us

  Please send us all questions, suggestions, and requests.

  MinhoLee@catholic.ac.kr

  Thank you.