. Author manuscript; available in PMC: 2024 Feb 1.

Published in final edited form as: Nat Comput Sci. 2023 Jul 31;3(8):700–708. doi: 10.1038/s43588-023-00496-1

Table 2.

Comparison of the True Positive Rate (TPR) of ORF annotation methods based on concordance with the GENCODE and RefSeq datasets. TPR was computed as the percentage of all ORFs in each dataset which were reconstracted identically by the method.

	GENCODE			RefSeq
	Execution Time (minutes)		TPR	Execution Time (minutes)		TPR
	Multi-threaded	Single-threaded	TPR	Multi-threaded	Single-threaded	TPR
ORFanage	0.28	0.6	0.88	0.33	1.1	0.94
TransDecoder	115	-	0.65	175	-	0.82
GeneMarkS-T	100	100	0.58	85	85	0.71

GeneMarkS-T times do not include conversion from reported format to genomic GTF style.