RNAalifold: improved consensus structure prediction for RNA alignments

BMC Bioinformatics

Table 2 Results on the RNA STRAND-Rfam dataset

RNA	comment	RIBOSUM	RNAalifold	Pfold	KNetFold	McC_mea
7SK		0.507	0.456	0.292	0.429	0.306
bicoid_3		0.949	0.840	n.a.	0.829	0.927
Corona_pk3	Pk	0.579	0.646	0.674	0.678	0.705
CPEB3_ribozyme	Pk	0.756	0.756	0.663	0.756	0.612
Gammaretro_CES		0.983	0.948	0.983	0.935	0.983
Hammerhead_1		1.000	0.474	0.621	0.831	0.614
Hammerhead_3		1.000	0.960	1.000	1.000	1.000
HDV_ribozyme	Pk	0.709	-0.018	0.784	0.388	0.396
IRES_c-myc		-0.004	0.079	0.286	-0.002	0.350
R2_retro_el		1.000	0.842	0.946	0.987	0.890
RNAIII		0.467	0.595	n.a.	0.479	0.830
RNase_MRP	Pk	0.626	0.423	0.457	0.271	0.575
rne5		0.994	0.969	0.975	0.762	0.923
RydC	Pk	0.466	0.562	0.608	0.466	-0.020
s2m		0.739	1.000	0.774	0.652	0.861
Telomerase-cil		1.000	0.937	0.921	1.000	0.953
Telomerase-vert	pk	0.918	0.751	n.a.	n.a.	0.820
Vimentin3		0.741	-0.016	0.184	0.771	0.629
Y		1.000	1.000	0.925	1.000	1.000
mean		0.759	0.651			0.703
mean	knetfold	0.750	0.645		0.680	0.696
mean	pfold	0.756	0.635	0.693	0.682	0.673

Performance comparisons on the RNA STRAND-Rfam dataset. We list the MCC for different alignments. Best performance indicated in bold, n.a. means that data is not available due to length restrictions on the respective server, pk denotes structures that contain a pseudo-knot. As there are many pseudo-knotted structures in this dataset, KNetFold was used in the "Check pseudoknot" mode. The MCCs take into account the pseudo-knots.

ISSN: 1471-2105