Table 4.

Detailed tool performance measures for 70% overlap. The sensitivity or true positive rate (TPR), specificity or true negative rate (TNR) and the F1 measure were calculated for each tool with each organism benchmark dataset (translatome). The sensitivity highlights how well the positive labels are detected and the specificity reveals how well negatively labeled ORFs are not predicted by the tools. The F1 measure is an unbiased tool accuracy measurement. The values were calculated with the requirement that the prediction of an ORF must be covered by at least 70% of its coding sequence

Organism	E. coli			L. monocytogenes			P. aeruginosa			S. typhimurium
measure	TPR	TNR	F1	TPR	TNR	F1	TPR	TNR	F1	TPR	TNR	F1
DeepRibo	0.83	0.97	0.90	0.96	0.37	0.91	0.94	0.84	0.94	0.77	0.98	0.86
REPARATION_blast	0.98	0.48	0.86	0.82	0.63	0.85	0.59	0.82	0.7	0.92	0.69	0.88
Ribo-TISH	0.02	0.96	0.05	0.02	0.96	0.05	0.04	0.95	0.07	0.1	0.95	0.17
IRSOM	0.52	0.53	0.58	0.42	0.51	0.54	0.62	0.3	0.65	0.5	0.53	0.58
SPECtre	0.39	0.54	0.48	—	—	—	0.03	0.82	0.05	0.04	0.77	0.07
smORFer	0.41	0.73	0.53	—	—	—	—	—	—	—	—	—
PRICE	0.12	0.98	0.21	0.2	0.96	0.33	0.54	0.88	0.68	0.27	0.99	0.43
ribotricer	0.92	0.34	0.81	1	0.01	0.89	0.95	0.17	0.83	0.95	0.43	0.84