Table 3.

Comparison of tRNAscan-SE prediction counts and search performance for selected model species. tRNA prediction counts for v1.3, and relative change for v2.0, show no difference or small gains in bacteria and archaea. In eukaryotes with large numbers of pseudogenes, the differences between v1.3 and v2.0 are much reduced after excluding pseudogenes. Search times of genomes using v1.3 and v2.0 show small changes of less than a minute or two for most genomes, depending on species, but notable improvements for large eukaryotic genomes (last three rows).

			tRNAscan-SE 1.3 / 2.0
Genome	Domain	Genome size (million bp)	Total tRNA predictions	tRNAs excluding pseudogenes	Search time
Bacillus subtilis 168	Bacteria	4.2	86/0	86/0	27s/+10s
Clostridioides difficile 630	Bacteria	4.3	87/+2	87/+1	19s/+18s
Escherichia coli K-12	Bacteria	4.6	88/+1	87/+1	43s/+5s
Mycobacterium tuberculosis H37Rv	Bacteria	4.4	45/0	45/0	40s/-17s
Pseudomonas aeruginosa PAO1	Bacteria	6.3	64/0	63/0	56s/-23s
Halobacterium sp.NRC-1	Archaea	2.0	47/0	47/0	1m 35s/-44s
Methanocaldococcus jannaschii	Archaea	1.7	37/0	37/0	29s/+13s
Pyrobaculum aerophilum	Archaea	2.2	45/+2	45/+2	1m 10s/+9s
Pyrobaculum calidifontis	Archaea	2.0	43/+3	43/+3	1m 43s/+26s
Pyrococcus furiosus DSM 3638	Archaea	1.9	46/0	46/0	33s/+24s
Sulfolobus acidocaldariusDSM 639	Archaea	2.2	49/+1	49/+1	47s/+14s
Saccharomyces cerevisiaeS288c	Eukaryota	12.2	275/0	275/0	52s/+1m 28s
Schizosaccharomyces pombe 972h-	Eukaryota	12.6	171/0	171/0	36s/+48s
Caenorhabditis elegans	Eukaryota	100.3	820/-99	609/+9	5m 9s/+30s
Drosophila melanogaster	Eukaryota	143.7	295/0	291/+1	3m 54s/+2m 18s
Arabidopsis thaliana	Eukaryota	119.7	639/+3	631/+3	4m 45s/+46s
Homo sapiens	Eukaryota	3101	625/-29	515/-4	1h 37m/-47m 23s
Mus musculus	Eukaryota	2731	26 287/+14 625	3296/+1201	7h 46m/-3h 13m
Zea mays	Eukaryota	2134	2296/-213	1464/-76	1h 5m/-19m 21s