Fig 1.
The RNA secondary structures at the 3′—terminus for 9 viruses.
(A) alfalfa mosaic virus AlMV-3, (B) citrus leaf rugose virus CiLRV-3, (C) tobacco streak virus TSV-3, (D) citrus variegation virus CVV-3, (E) apple mosaic virus APMV-3, (F) lilac ring mottle virus LRMV-3, (G) prune dwarf ilarvirus PDV-3, (H) elm mottle virus EMV-3, and (I) asparagus virus 2 AVII.
Table 1.
The definition of three maps φ1, φ2, and φ3.
Fig 2.
Three characteristic curves of TSV-3.
(A) M-K curve, (B) R-Y curve, and (C) W-S curve. Let G = g1g2g3…gn be the characteristic sequence of TSV-3, where n is the length of G. Each base gi can be mapped into three dots φ1(gi) = (x1i, y1i, z1i), φ2(gi) = (x2i, y2i, z2i), and φ3(gi) = (x3i, y3i, z3i), where i = 1, 2, …, n. By connecting dots in φ1(gi) = (x1i, y1i, z1i) (i = 1, 2, …, n) in order, we can obtain an M-K curve to represent the characteristic sequence G. Similarly, by connecting dots in φ2(gi) = (x2i, y2i, z2i) and φ3(gi) = (x3i, y3i, z3i) respectively, we can obtain R-Y and W-S curves.
Table 2.
The similarity/dissimilarity matrix for nine RNA secondary structures in Fig 1 based on RNA 36D vector representation.
Fig 3.
The phylogenetic tree for nine virus in Fig 1.
The tree was constructed using UPGMA, in which the distance matrix is calculated by our RNA comparison method based on 36D vector representation.
Fig 4.
The phylogenetic tree for RNA secondary structures in S1 Fig.
Branch colors indicate six clusters of RNase P structures from RNase P database and five clusters of pseudo-knot structures from Pseud Base. The six clusters of RNase P structures include: (1) Gamma Purple Bacteria RNase P structures, (2) Green sulfur Bacteria RNase P structures, (3) Low G+C Gram positive RNase P structures, (4) Cyanobacterial RNase P structures, (5) Archaea Euryarchaeal RNase P structures, and (6) Nuclear RNase P structures.
Fig 5.
The phylogenetic tree for non-coding RNA secondary structures in S2 Fig.
The 18 branch colors represent 18 non-coding RNA families respectively from RNAstrand database, including 5S rRNA (RF00001), Gammaretro_CES (RF00374), Hepatitis delta virus ribozyme (RF00094), Vimentin3 (RF00109), Corona_pk3 (RF00165), Y_RNA (RF00019), s2m (RF00164), Hammerhead ribozyme (type III) (RF00008), Ciliate telomerase RNA (RF00025), R2 RNA element (RF00524), Hammerhead ribozyme (type I) (RF00163), Vertebrate telomerase RNA (RF00024), rne5 (RF00040), RNase MRP (RF00030), 7SK RNA (RF00100), RNAIII (RF00503), RydC RNA (RF00505), and Bicoid 3 prime-UTR regulatory element (RF00551).