tRNAscan-SE identifies transfer RNA genes in genomic DNA or RNA sequences. It combines the specificity of the Cove probabilistic RNA prediction package (Eddy & Durbin, 1994) with the speed and sensitivity of tRNAscan 1.3 (Fichant & Burks, 1991) plus an implementation of an algorithm described by Pavesi and colleagues (1994) which searches for eukaryotic pol III tRNA promoters (our implementation referred to as EufindtRNA). tRNAscan and EufindtRNA are used as first-pass prefilters to identify “candidate” tRNA regions of the sequence. These subsequences are then passed to Cove for further analysis, and output if Cove confirms the initial tRNA prediction. In this way, tRNAscan-SE attains the best of both worlds:

  • a false positive rate of less than one per 15 billion nucleotides of random sequence
  • the combined sensitivities of tRNAscan and EufindtRNA (detection of 99% of true tRNAs)
  • search speed 1,000 to 3,000 times faster than Cove analysis and 30 to 90 times faster than the original tRNAscan 1.3 (tRNAscan-SE uses both a code-optimized version of tRNAscan 1.3 which gives a 650-fold increase in speed, and a fast C implementation of the Pavesi et al. algorithm).

This program and results of its analysis of a number of genomes have been published in Lowe & Eddy, Nucleic Acids Research 25: 955-964 (1997).