A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Table 1

Alignment times of BinaryPartialAlign, IncrementalPartialAlign, and classical SW.

	Alignment time			Base error in estimated deletion position
	(mean ± standard deviation in msec)			(mean ± standard deviation in bp)
Sequence length	BinaryPartialAlign	IncrementalPartialAlign	Classical SW	BinaryPartialAlign	IncrementalPartialAlign	Classical SW
100–199	226.7 ± 95.2	3149.0 ± 2460.3	106.6 ± 22.4	9.8 ± 12.3	12.9 ± 11.1	38.6 ± 40.6
200–299	418.3 ± 148.0	6896.9 ± 5484.0	176.1 ± 21.6	13.1 ± 12.3	23.7 ± 20.3	67.1 ± 73.0
300–399	611.0 ± 203.1	16295.1 ± 13346.4	241.4 ± 21.1	21.8 ± 22.8	37.1 ± 30.2	76.0 ± 96.8
400–499	741.6 ± 237.1	28763.0 ± 20988.4	247.0 ± 63.4	29.3 ± 27.9	51.9 ± 33.4	85.9 ± 95.8
500–599	798.8 ± 259.6	38638.7 ± 29724.3	284.3 ± 85.2	37.4 ± 38.9	69.4 ± 50.3	92.2 ± 99.5
600–699	932.9 ± 327.4	60640.8 ± 44106.5	321.3 ± 106.3	41.5 ± 41.1	83.2 ± 53.2	107.6 ± 123.9
700–799	1177.9 ± 413.2	71953.8 ± 59874.8	359.1 ± 128.7	46.2 ± 35.7	94.0 ± 59.8	125.4 ± 167.5
800–899	1241.5 ± 432.4	81953.1 ± 64055.2	395.1 ± 148.0	51.6 ± 46.7	102.9 ± 59	143.7 ± 205.3
900–999	1366.1 ± 482.5	117779.0 ± 84950.1	679.1 ± 33.6	50.9 ± 52.1	127.2 ± 72.5	242.4 ± 285.8