Table 1.

Statistics characterizing the GeneMarkS-T initial gene predictions made in assembled transcripts as well as the HC genes predicted by the GeneMarkS-TP module. Two versions of a reference protein database were used for each species: the ‘Species excluded’, as well as the ‘Order excluded’ (see Data Sets). Refinement made by GeneMarkS-TP reduced the number of initial predictions and produced a significant increase in Pr. In most of the genomes there was also a positive change in Sn, especially in large inhomogeneous genomes of G. gallus and M. musculus. Additional data is provided in Supplemental Table S1.

Species	# of genes initially predicted by GeneMarkS-T	Sn/Pr of GeneMarkS-T predicted genes	Order excluded DB		Species excluded DB
			# of HC genes	Sn/Pr of HC genes	# of HC genes	Sn/Pr of HC genes
C. elegans	14,746	46.8 / 63.4	8,062	35.7 / 88.4	11,399	51.7 / 90.6
A. thaliana	17,589	51.2 / 79.9	16,008	56.7 / 97.3	16,551	58.8 / 97.6
D. melanogaster	10,163	59.6 / 81.8	8,109	55.0 / 94.7	9,223	63.7 / 96.3
S. lycopersicum	19,526	68.0 / 78.4	17,231	75.1 / 95.3	17,489	75.8 / 95.2
D. rerio	22,992	59.6 / 59.9	16,918	67.0 / 88.5	16,573	66.9 / 90.4
G. gallus	17,381	49.6 / 47.0	12,473	74.4 / 89.1	12,564	74.0 / 88.4
M. musculus	15,819	49.6 / 63.2	13,057	63.5 / 93.2	12,965	63.9 / 94.5