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Basic information
Short name STADIUM
Full name Species-specific tRNA adaptive index compendium
Description STADIUM provides not only stAI value of each gene, but also provides statistics based on pathway-based classification.
URL http://stadium.pmrc.re.kr
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted Catholic University of Korea
Address
City
Province/State
Country/Region Korea, Republic of
Contact name Minho Lee
Contact email MinhoLee@catholic.ac.kr
Data information
Data object
  • Animal
Data type
  • DNA
  • Protein
Database category
  • Gene genome and annotation
  • Pathway
Major organism
  • NA
Keyword
  • tRNA adaptation
Publications
  • STADIUM: Species-Specific tRNA Adaptive Index Compendium. [PMID: 30602089]
    Jonghwan Yoon, Yeun-Jun Chung, Minho Lee

    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.

     Genomics Inform 2018:16(4)

    0 Citations (from Europe PMC, 2019-01-19)

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Record metadata

  • Created on: 2019-01-15
    • ***ina@***c.cn [2019-01-23]
    • ***d@***c.cn [2019-01-15]
    • ***d@***c.cn [2019-01-15]
    • ***d@***c.cn [2019-01-15]

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