Table 2.

Runtimes and internal space requirements for finding MUMs. We compared MUMmer 3.19 [8], MGA [9], and SeqAn for different DNA sequences on a 3.2 GHz Intel Xeon computer with 3 GB of internal memory running Linux. Because MUMmer finds MUMs of not more than two sequences, its results on the Chlamydia and Escherichia coli strains are left empty. For the last dataset, we used SeqAn's external memory data strutures to limit the internal memory consumption.

Species		MUMer		MGA		SeqAn
	size (Mbp)	time (m:s)	space (MB)	time (m:s)	space (MB)	time (m:s)	space (MB)
C. trachomatis D/UW-3/CX	1.043
C. muridarum Nigg	1.073	-	-	0:06	33.8	0:04	31.6
C. trachomatis A/HAR-13	1.044
E. coli K12	4.640
E. coli O157:H7 str. Sakai	5.498
E. coli CFT073	5.231	-	-	105:40	353.5	0:58	304.6
E. coli UTI89	5.066
E. coli 536	4.939
E. coli APEC O1	5.082
H. sapiens (chr. 21)	46.94	2:25	568	4:44	1188	4:06	1307
M. musculus (chr. 16)	98.25
H. sapiens (chr. 16)	98.25	2:55	1362	18:48	1500	5:38	1627
P. troglodytes (chr. 16)	88.83
						external string
H. sapiens (chr. 1)	247.2	insufficient memory		insufficient memory		66:20	510
M. musculus (chr. 1)	197.1