ArticleGenomics & informatics2018
STADIUM: Species-Specific tRNA Adaptive Index Compendium.
Article in Genomics & informatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 20 citations in OpenAlex.
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- Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules.Nature genetics · 2024Article
- A spatiotemporally resolved atlas of mRNA decay in thebioRxiv : the preprint server for biology · 2024Article
- mRNA stability and mMolecular cell · 2023Article
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- Article
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- Causes and Consequences of Purifying Selection on SARS-CoV-2.Genome biology and evolution · 2021Article
- Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.Nature methods · 2021Article
- In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species.PLoS computational biology · 2020Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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