Genomics Inform.  2018 Dec;16(4):e28. 10.5808/GI.2018.16.4.e28.

STADIUM: Species-Specific tRNA Adaptive Index Compendium

• Yoon J
• Chung YJ
• Lee M

• KMID: 2439218
• DOI: http://doi.org/10.5808/GI.2018.16.4.e28

Abstract

Due to the increasing interest in synonymous codons, 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 is calculated based on the abundance of intracellular tRNA and the binding strength between a codon and a tRNA. The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species. Although a subsequently developed webserver (stAIcalc) provided tools that calculated stAI values, it was not available to access pre-calculated values. In addition to about 100 species in 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 the stAI value of each gene but also statistics based on pathway-based classification. The database is expected to help researchers who have interests in codon optimality and the role of synonymous codons. STADIUM is freely available at http://stadium.pmrc.re.kr.

Keyword

codon optimality; KEGG pathway; Shiny; tRNA adaptive index

MeSH Terms

Classification
Clinical Coding
Codon
Evolution, Molecular
Genes, vif
Genetics
Pharmacology
RNA, Transfer*
Codon
RNA, Transfer