Table 4 Comparison of running time (in seconds) for RNA FRABASE (version 2), FASTR3D, R3D-BLAST, RAG-3D and R3D-BLAST2
From: R3D-BLAST2: an improved search tool for similar RNA 3D substructures
Query RNA | R3D-BLAST2 | R3D-BLAST | RAG-3D | RNA FRABASE | FASTR3D |
|---|---|---|---|---|---|
Pseudoknot | 4.5 | 2.8 | 41.7 | 1.2 | 2.8 |
Riboswitch | 0.8 | 0.5 | 2.9 | 1.0 | 0.3 |
Ribozyme | 0.8 | 0.5 | 42.2 | 0.7 | 0.3 |
tRNA | 11.9 | 2.3 | 2.7 | 1.9 | 0.3 |
5S rRNA | 5.4 | 3.0 | 49.0 | 1.0 | 0.6 |
12S rRNA | 29.6 | 17.6 | 12.4 | 6.5 | 0.7 |
16S rRNA | 26.9 | 15.6 | 12.6 | 7.0 | 0.6 |
18S rRNA | 38.5 | 23.0 | 28.2 | 4.4 | 1.0 |