RefSelect: a reference sequence selection algorithm for planted (l, d) motif search

BMC Bioinformatics

Table 6 Assessment of RefSelect on large data sets

t	k	DNA Sequences			Protein Sequences
t	k	time	time ^a	N _original /N _improved	time	time ^a	N _original /N _improved
50	3	0.5 s	0.4 s	2.37	0.4 s	0.4 s	15.79
100	5	2.0 s	1.9 s	2.56	1.8 s	1.7 s	15.41
200	10	8.2 s	8.0 s	1.85	7.3 s	7.1 s	14.20
300	15	18.6 s	18.1 s	2.43	16.2 s	15.9 s	18.31
400	20	33.5 s	32.5 s	2.52	28.7 s	27.9 s	18.42
500	25	52.4 s	50.6 s	2.78	44.9 s	43.5 s	16.64
600	30	75.8 s	73.5 s	2.56	66.8 s	64.8 s	15.98

s: seconds; time and time ^a: the running time of RefSelect and that of the first step of RefSelect; N _original and N _improved: the number of candidate motifs generated from the first k original input sequences and that for the k reference sequences selected by RefSelect.

ISSN: 1471-2105