BMC Research Notes

Table 3 Sequence summary and resource usage for tree construction and traversal of test datasets

From: Suffix tree searcher: exploration of common substrings in large DNA sequence sets

		Tree construction				Full traversal
Dataset	Size (Mbp)	Time¹	Rate (kbp/s)	Peak memory (Gbp)	Disk usage	Time	Peak memory (Mbp)
10 random 10 kbp seqs	0.1	154 ms	649.4	1.72	4.0 Mb	21 ms	2.3
100 random 10 kbp seqs	1.0	733 ms	1,364.3	1.72	39.7 Mb	150 ms	22.9
1,000 random 10 kbp seqs	10.0	9.2 s	1,084.9	1.72	397.1 Mb	3.8 s	24.0
10,000 random 10 kbp seqs	100.0	1 m 56 s	861.3	1.72	3.9 Gb	5 m 10s	24.1
100,000 random 10 kbp seqs	1,000.0	29 m 52 s	558.1	1.72	38.8 Gb	7 h 23 m	25.2
10,000 random 100 bp seqs	1.0	6.0 s	166.4	1.72	111.6 Mb	1.7 s	22.0
10,000 random 1 kbp seqs	10.0	13.7 s	732.1	1.72	459.7 Mb	25.5 s	24.1
10,000 random 100 kbp seqs	1,000.0	25 m 42 s	648.6	1.72	38.5 Gb	51 m 22 s	24.3
10,000 random 1 Mbp seqs²	10,000.0	12 h 29 m	222.5	1.72	384.7 Gb	9 h 18 m	24.0
62 E. coli genomes	310.5	21 m 55 s	235.7	1.72	11.9 Gb	2 m 33 s	24.0
62 random seqs w/ E. coli lengths	310.5	7 m 3 s	734.0	1.72	11.9 Gb	2 m 56 s	24.0
4 Chlorella virus genomes	0.9	815 ms	1,074.5	1.72	41.8 Mb	203 ms	24.0
Human genome (hg38)²	3,209.3	3 h 58 m	223.7	2.07	117.2 Gb	45 m 33 s	24.1

¹Tree construction time includes time to both Import sequences and Build the suffix index.
²The "10,000 random 1 Mbp" and human genome datasets utilized an external USB2.0 hard drive.

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ISSN: 1756-0500

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