RAPSearch: a fast protein similarity search tool for short reads

BMC Bioinformatics

Table 3 Performance comparison of similarity search tools on the same query dataset (4440037) against different protein similarity search databases.

Database	Total sequences	Total aa	Running time (CPU hours)		Reads with homologs found in the protein database (E-value cutoff = 1e-3)
			BLAST	RAPSearch	Overlap	BLAST-only	RAPSearch-only
Extended COG ^a	670,804	215,687,522	27.5	0.6	6384 (94.4%)	259 (3.8%)	123 (1.8%)
IMG	4,054,690	1,231,432,735	154	3.5	9,791 (95.3%)	270 (2.6%)	213 (2.1%)
NR ^b	8,994,603	3,078,807,967	428	9.7	10546 (95.5%)	256 (2.3%)	238 (2.2%)

^a: Extended COG contains sequences collected in eggNOG database; ^b: NR is the NCBI non-redundant database. The total number of sequences and amino acids included in each database are shown in the "Total sequences" and "Total aa" columns, respectively.

ISSN: 1471-2105