RNA motif search with data-driven element ordering

BMC Bioinformatics

Table 2 The running times (in seconds) of different programs searching for various descriptors in the whole human genome

	ATP apt.	GTP apt.	generalized	HHR-I	HHR-II	HHR	HDV	HDV	HDV
		class I	tRNA	(4 bp)	(3 bp)	extended	(loose P4)	(stem P4)	(mispairs)
RNAbob	3,419.03	2,744.30	7,450.07	923.53	5,027.33	2,269.35	209,932.57	43,430.78	36,459.87
RNAmotif	80.78	222.54	7,374.32	87.69	265.09	116.15	26,259.79	2,513.90	9,240.83
RNAMot	unf	unf	unf	unf	unf	unf	unf	4,538.92	8,925.31
RNArobo	80.91	151.09	250.63	96.48	110.64	108.46	171.16	169.90	111.30
RNArobo-ins	–	153.38	–	98.22	137.47	–	173.82	171.54	–

Experiments were run on Intel Xeon E5520 CPU. RNArobo-ins is RNArobo run with modified descriptors allowing insertions in helical elements. RNAMot did not finish on most of the inputs within time limit of three days. Only results that finished within three days are shown. Since DDEO is randomized, we show the average running time of five runs of RNArobo. Standard deviation was up to 3 % or 5 sec, with the exception of the HHR extended descriptor, where the running time ranged from 98 to 125 sec
Boldface numbers represent the best running times for a particular descriptor

ISSN: 1471-2105