tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences

Methods Mol Biol. 2019;1962:1-14. doi: 10.1007/978-1-4939-9173-0_1.


Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.

Keywords: Covariance model; Gene prediction; Non-coding RNA; RNA secondary structure; Transfer RNA.

MeSH terms

  • Data Display
  • Databases, Genetic
  • Eukaryotic Cells
  • Genomics / methods*
  • Internet
  • Models, Genetic
  • RNA, Transfer / genetics*
  • Software*


  • RNA, Transfer