Table 2. Summary of gene identification and annotation of assembled catfish contigs based on BLAST homology searches against various protein databases (Zebrafish, UniProt, nr).

	Trans-ABySS			Trinity
	Zebrafish	UniProt	nr	Zebrafish	UniProt	nr
Contigs with putative gene matches	60,892	50,766	64,788	82,365	68,797	83,972
Annotated contigs ≥500 bp	41,313	37,468	44,019	71,782	61,658	73,849
Annotated contigs ≥1000 bp	29,023	27,479	30,379	59,986	53,210	61,185
Unigene matches	16,610	19,341	25,416	17,892	19,970	26,549
Hypothetical gene matches	986	0	3,788	1,058	0	3,693
Quality Unigene matches	14,679	15,933	15,863	15,821	15,427	20,589

Putative gene matches were at E-value ≤ 1e-5. Hypothetical gene matches denote those BLAST hits with uninformative annotation. Quality unigene hits denote more stringent parameters, including score ≥100, E-value ≤ 1e-20.