Table 4.

Comparison of running times

Query set	Database	Program	Parameters	Time
				Indexinga	Search	Alignment
Uniprot	uniprot	SANS	W = 100	3 h 22 m	30 h 4 m	2 h 19 m
Metagenome	swissprot	BLAST	–b 250		380 d
		USEARCH	a = 1 r = 8		19 h 55 m
		SANS	W = 1	57 m	13 m	48 m
	uniprot	SANS	W = 1	4 h 52 m	28 m	32 m
Genome	uniprot	SSEARCH	–s BL62 –f −11 –g −1 –E 1.0 –m 9C –z 3 –d 0		640 d
		BLAST	–b 1000		100 h
		parallel BLAST	10 processors, –b 1000		max 13 h / processor
		SANS	W = 100	3 h 57 m	12 m	10 m
			W = 1000		23 m	52 m
			W = 2000		33 m	1 h 40 m

^aIndexing time includes indexing both the query set and database from scratch.