Table 2. Newly found RNA motifs and their prediction classes.
For motifs less than or equal to 10 vertices, motifs include updates since our 2011 RAG version. For motifs larger than 10 vertices, motifs are new. Many of the newly found graph motifs are classified as RNA-like. A few of them are misclassified as non-RNA-like, but those motifs only have a single RNA each. For example, there are 4 RNAs found for ID 9_4, which are RNA-like, but only 1 for ID 9_46, which is non-RNA-like. The larger RNA motifs more than 11 vertices include only new data. Although there are some misclassified data for 11 vertices, the other results for 12 and 13 nodes are very good. Only one RNA graph, 11_24, has 2 RNAs, and it is properly predicted as RNA-like.
| Graph ID | Label | RNA (PDB ID) |
|---|---|---|
| 8_15 | RNA-like | Ribonuclease P RNA (1NBS_A), 18S ribosomal RNA (3J16_K) |
| 9_2 | RNA-like | Group I Intron (1GID_A,1GID_B,1HR2_B) |
| 9_4 | RNA-like | 80S ribosomal RNA (3IZD_A) |
| 9_19 | RNA-like | Signal Recognition Particle (1L9A_B,1MFQ_A,2GO5_A,2J37_A) |
| 9_46 | non-RNA-like | Ribonuclease P Bacterial A-type (2A2E_A) |
| 10_4 | RNA-like | M-Box Riboswitch Aptamer Domain (2QBZ_X) |
| 10_19 | RNA-like | Glycine Riboswitch (3P49_A) |
| 10_45 | non-RNA-like | Adenosylcobalamin Riboswitch (4GMA_Z) |
|
| ||
| 11_1 | RNA-like | 23S ribosomal RNA (3J5S_A) |
|
| ||
| 11_24 | RNA-like | M-box riboswitch (3PDR_A,3PDR_X) |
|
| ||
| 11_56 | RNA-like | Ribonuclease P (1U9S_A) |
|
| ||
| 11_89 | non-RNA-like | Transfer-messenger RNA (3IYQ_A) |
|
| ||
| 11_138 | RNA-like | Group 1 Intron (3BO4_B) |
|
| ||
| 11_177 | RNA-like | Ribonuclease P (1NBS_B) |
|
| ||
| 11_207 | non-RNA-like | RNase P (3DHS_A) |
|
| ||
| 11_216 | non-RNA-like | Group I intron with a tyrosyl-tRNA synthase (2RKJ_C) |
|
| ||
| 12_150 | RNA-like | tetrahymena ribozyme (1GRZ_A) |
|
| ||
| 12_286 | RNA-like | 80S ribosomal RNA (3ZEX_E) |
|
| ||
| 12_387 | RNA-like | Group I intron (3IIN_B) |
|
| ||
| 12_392 | RNA-like | Group I intron (3BO2_BCDE) |
|
| ||
| 13_140 | RNA-like | Adenosylcobalamin riboswitch (4GXY_A) |
|
| ||
| 13_181 | RNA-like | tetrahymena ribozyme (1GRZ_B) |
|
| ||
| 13_1021 | RNA-like | Group I intron (1U6B_CDB) |
|
| ||
| 13_1047 | RNA-like | Group I intron (3BO3_CDB) |
|
| ||
| 13_1154 | non-RNA-like | Group I intron-product complex (1Y0Q_A) |
|
| ||
| 13_1213 | RNA-like | 28S ribosomal RNA (3J16_J) |