Efficient alignment of RNA secondary structures using sparse dynamic programming

BMC Bioinformatics

Table 1 Comparison on running time of ERA, LocARNA , and RNAforester

RNA family	length	num.	ERA	LocARNA	ERA vs.	RNAforester	ERA vs.
	(bp)	pairs	(sec)	(sec)	LocARNA (fold)	(sec)	RNAforester (fold)
tRNA	78	21	0.017	0.100	5.882	0.047	2.765
Gly riboswitch	105	22	0.015	0.277	18.46	0.162	10.80
U12 spliceosome	160	42	0.035	0.311	8.886	0.657	18.77
Phage_pRNA	244	43	0.124	0.647	5.218	6.935	55.93
tmRNA	367	64	0.929	22.45	24.16	225.4	242.6
biocoid_3UTR	549	155	4.898	170.3	34.77	13.99	2.856
snR86	1004	333	53.15	4862	91.48	5.579	-9.527 ∗
Sacc_telomerase	1162	181	23.93	522.3	21.82	3697	154.5

ISSN: 1471-2105