STELLAR: fast and exact local alignments

BMC Bioinformatics

Table 2 Running times and sensitivity on simulated sequences of different lengths

seq length	1 kb		10 kb		100 kb		1 Mb		10 Mb
	time	missed	time	missed	time	missed	time	missed	time	missed
SSEARCH	2.45 s	0.00%	259.5 s	0.00%	7:16 h	0.00%	136:16 h	0.00%	–	–
STELLAR	1 ms	0.00%	5 ms	0.00%	0.07 s	0.00%	4.36 s	0.00%	782.46 s	0.00%
BWT-SW	–	–	787 ms	0.00%	1.40 s	0.00%	16.33 s	0.00%	508.45 s	0.00%
BLAST	4 ms	14.00%	8 ms	6.00%	0.03 s	11.40%	0.25 s	13.40%	3.34 s	12.64%
BLAST*	6 ms	0.00%	13 ms	0.00%	0.16 s	0.00%	14.75 s	0.60%	2266.64 s	1.46%
LASTZ	9 ms	10.00%	59 ms	2.00%	0.56 s	7.80%	5.99 s	9.40%	116.26 s	9.12%
BLAT	25 ms	0.00%	39 ms	0.00%	0.40 s	1.00%	15.24 s	33.00%	384.79 s	69.30%

Sequences contain a = [length/2000] local alignments with a maximal error rate of 10% and lengths between 50 and 200 bp. The simulation of the 1 kb sequences was repeated 50 times, the simulation of the 10 kb and 100 kb sequences ten times. The displayed values are the average of all runs except for SSEARCH which was run only once. Sensitivity is measured by the percentage of missed local alignments (Fig. 8). BWT-SW, BLAST, BLAT, and LASTZ were run with default parameter settings. BLAST* stands for a more sensitive run of BLAST with the word size parameter set to s^min, i.e. the minimal length of an ε-core (see text for details).

ISSN: 1471-2105