Table 2. Whole genome tRNA detection rates for ARAGORN and tRNAscan-SE^a.

Lineage	Genome	No. of tRNAs detected		Search time (s)b
		ARAGORNc	tRNAscan-SEd	ARAGORNc	tRNAscan-SEd
Archaea	M.jannaschii	37	37	1.4	With –A 24
Bacteria	E.coli O157:H7	104	103	5.2	With –B 112
Eukaryota	S.cerevisiae	274	275	11	Default 114

^atRNAscan-SE version 1.23.

^bTested on an AMD Athlon, 1.6 GHz, 1024 Mb RAM with Linux.

^cARAGORN run with a maximum intron size of 100 nucleotides and the –t switch (tRNA detection only). The intron size roughly corresponds to the default used by tRNAscan-SE.

^dThe –A and –B switches invoke the specific covariance model for each lineage. This increases the search time. Run with –G (general model), the search time decreases to 15 s for M.jannaschii and 43 s for E.coli. However, in E.coli, the number of tRNAs detected decreases by 1. The default model in tRNAscan-SE is the eukaryotic model.