R3D-BLAST2: an improved search tool for similar RNA 3D substructures

BMC Bioinformatics

Table 3 Search results of RNA FRABASE (version 2), FASTR3D, R3D-BLAST, RAG-3D and R3D-BLAST2

Query RNA	R3D-BLAST2				R3D-BLAST	RAG-3D	RNA	FASTR3D
	100%	≥90%	< 90%	Total			FRABASE
Pseudoknot	2	608	112	720 (1.0)	384 (1.0)	58 (1.9)	204 (0.7)	232 (0.7)
Riboswitch	11	45	20	65 (2.1)	53 (1.5)	10 (0.7)	1 (0.0)	1 (0.0)
Ribozyme	7	13	63	76 (1.2)	40 (1.8)	60 (0.2)	12 (0.5)	10 (0.4)
tRNA	78	397	1071	1468 (2.4)	560 (2.6)	10 (0.3)	59 (2.2)	19 (1.3)
5S rRNA	64	70	687	757 (2.2)	428 (2.0)	100 (0.1)	26 (0.3)	21 (0.3)
12S rRNA	2	2	7817	7819 (2.1)	3784 (2.0)	0 (0.0)	1 (0.0)	1 (0.0)
16S rRNA	1	132	4931	5063 (2.5)	2857 (2.7)	0 (0.0)	0 (0.0)	1 (0.0)
18S rRNA	1	7	8265	8272 (2.4)	4201 (2.2)	0 (0.0)	0 (0.0)	1 (0.0)

In the column titles of R3D-BLAST2, the percentage denotes the query coverage that equals to the percent of the query length in the alignment. The values presented in the parentheses indicate the average RMSD values (Å) between the structural hits and query, where notably the RMSD value returned by RAG-3D is calculated based on two superimposed RNA 3D graphs, rather than based on two superimposed RNA 3D structures as the other tools do

ISSN: 1471-2105