STELLAR: fast and exact local alignments

BMC Bioinformatics

Table 1 Running times and sensitivity on simulated sequences containing local alignments of different error rates

error rate	0%		2.5%		5%		7.5%		10%
	time	missed	time	missed	time	missed	time	missed	time	missed
SSEARCH	133:17 h	0.00%	132:55 h	0.00%	133:24 h	0.00%	132:25 h	0.00%	132:52 h	0.00%
STELLAR	2.96 s	0.00%	3.30 s	0.00%	3.61 s	0.00%	3.91 s	0.00%	4.44 s	0.00%
BWT-SW	16.59 s	0.00%	16.63 s	0.00%	16.53 s	0.00%	16.29 s	0.00%	16.24 s	0.00%
BLAST	0.25 s	0.00%	0.26 s	0.16%	0.26 s	5.36%	0.25 s	17.00%	0.24 s	38.80%
BLAST*	0.25 s	0.16%	0.26 s	0.00%	0.28 s	0.04%	0.51 s	0.28%	14.99 s	2.60%
LASTZ	6.49 s	0.00%	6.48 s	0.72%	6.22 s	5.56%	5.86 s	12.68%	5.23 s	24.92%
BLAT	14.30 s	29.36%	11.52 s	29.64%	14.06 s	28.88%	14.71 s	31.44%	14.66 s	34.32%

Sequences have a length of 1 Mb and contain local alignments of lengths between 50 and 200 bp. The simulations were repeated five 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