Table 3.

Comparison with A. pisum gene models

	#genes	#ESTs
Hit category		5′-ESTs	3′-ESTs
RefSeq	7,390	44,161	34,462
ab initio*	1,058	2,741	1,975
no hit to models		3,089	11,400
_potential connection with model**	NA	984	8,372
novel gene***	248+	432+	432+
_unmapped****	NA	200	767

^*ab initio: non-Refseq NCBI Gnomon gene models

^**This category represents the EST that does not match any gene models, but the other end of the clone does match. Such “no hit” EST should connect with the gene models that the counterpart overlaps. The matching failure of one of the pair may be due to the incomplete gene model.

^***Novel genes predicted in this study (Table S1) are counted. Note that this prediction was restricted to the clones with “well-paird mapping” ESTs and there must be more genes that are not undocumented in the reference gene models.

^****ESTs that do not map to the genome.