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STADIUM: Species-Specific tRNA Adaptive Index Compendium.

Jonghwan Yoon1, Yeun-Jun Chung2,3, Minho Lee3

  • 1Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.

Genomics & Informatics
|January 3, 2019
PubMed
Summary

The tRNA adaptation index (tAI) measures gene translational efficiency. A new database, STADIUM, now provides easy access to species-specific tRNA adaptation index (stAI) values for 148 species, aiding codon bias research.

Keywords:
KEGG pathwayShinycodon optimalitytRNA adaptive index

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Synonymous codons and codon bias are increasingly studied.
  • The tRNA adaptation index (tAI) measures translational efficiency based on tRNA abundance and codon-tRNA binding.
  • The specific tRNA adaptation index (stAI) was developed to account for species-specific tRNA copy numbers.

Purpose of the Study:

  • To provide researchers with easy access to pre-calculated stAI values.
  • To expand the number of species with available stAI data beyond existing tools.
  • To create a centralized resource for codon optimality and synonymous codon research.

Main Methods:

  • Calculated stAI values for the coding sequences of 148 species.
  • Developed a novel web database named STADIUM (Species-specific tRNA adaptive index compendium).
  • Integrated pathway-based classification for statistical analysis within the database.

Main Results:

  • STADIUM provides stAI values for each gene across 148 species.
  • The database includes pathway-based statistics for enhanced analysis.
  • Expanded stAI data availability significantly beyond previous resources.

Conclusions:

  • STADIUM offers a valuable, accessible resource for researchers studying codon bias and translational efficiency.
  • The database facilitates deeper investigation into the role of synonymous codons in various biological contexts.
  • STADIUM is freely available at http://stadium.pmrc.re.kr.