Table 1.

Clustering of different data-sets of small, medium and large sized protein sequences using different methods

Small proteins (10–100 amino acids length)
Number of sequences - 500
Method	# of clusters	Threshold	Word-length	Time
CW	15	0.5	NA	0 m 11.835 s
k-tuple	3	0.5	2	0 m 1.539 s
CLAP	7	0.5	5	2 m 28.322 s
CLUSS	68	NA	4	0 m 11.000 s
CD-HIT	223	0.5	3	0 m 0.034 s
Small proteins (10–100 amino acids length)
Number of sequences - 1000
Method	# of clusters	Threshold	Word-length	Time
CW	23	0.5	NA	0 m 59.788 s
k-tuple	3	0.5	2	0 m 5.659 s
CLAP	17	0.5	5	9 m 52.099 s
CLUSS	NA	NA	NA	0 m 11.000 s
CD-HIT	607	0.5	3	0 m 0.091 s
Medium proteins (400–600 amino acids length)
Number of sequences - 500
Method	# of clusters	Threshold	Word-length	Time
CW	2	0.5	NA	8 m 46.895 s
k-tuple	3	0.5	2	0 m 2.25 s
CLAP	3	0.5	5	2 m 50.918 s
CLUSS	95	NA	4	0 m 3.133 s
CD-HIT	227	0.5	3	0 m 0.592 s
Medium proteins (400–600 amino acids length)
Number of sequences - 1000
Method	# of clusters	Threshold	Word-length	Time
CW	5	0.5	NA	32 m 50.379 s
k-tuple	2	0.5	2	0 m 7.789 s
CLAP	7	0.5	5	11 m1 2.664 s
CLUSS	NA	NA	NA	NA
CD-HIT	708	0.5	3	0 m 3.281 s
Large proteins (850–1000 amino acids length)
Number of sequences - 500
Method	# of clusters	Threshold	Word-length	Time
CW	15	0.5	NA	42 m 1.184 s
k-tuple	4	0.5	2	0 m 2.91 s
CLAP	4	0.5	5	4 m 22.752 s
CLUSS	NA	NA	NA	NA
CD-HIT	125	0.5	3	0 m0.916 s

The processing time was computed using the workstation that hosts the CLAP web-server, with a 2.40 GHz, Intel xeon processor and 16GB RAM running CentOS. The number of clusters generated at a specific threshold and word-length used in the computations is also shown.