Table 1.
Lists of J99 methylation motifs obtained using different methylation motif detection approaches.a
| PacBio + MotifMaker | ONT + Snapper (raw output) | ONT + Tombo | ONT + Nanodisco | Total number in genome (±strand) |
|---|---|---|---|---|
| GAGG | GAGG | GAGG | 2542/2462 | |
| GTSAC | GTCAC, GTGACb | 104/104 | ||
| GATC | GATC | GATC | 5499/5499 | |
| TCGA | TCGA | 340/340 | ||
| CCGG | CCGG | CCGG | 1807/1807 | |
| ATTAAT | ATTAAT | ATTAAT | ATTAAT | 426/426 |
| CCNNGG | CCNNGG | CCNNGG | 1193/1193 | |
| GTAC | GTAC | GTAC | 182/182 | |
| CGWCG | CGACG, CGTCGb | CGWCG | 264/264 | |
| GANTC | GANTC | GANTC | 2756/2756 | |
| GCGC | GCGC | GCGC | GCGC | 6104/6104 |
| CATG | CATG | CATG | CATG | 7567/7567 |
| GCCTA | GCCTA | GCCTA | GCCTA | 1532/1532 |
| GWCAY | GACAY, GTCAT, GTCACb | GACAC | GWCAY | 2641/2464 |
| GGWCNA | GGWCNA | GGWCHA | 838/789 | |
| TCNNGA | 1949/1949 |
It should be noted here that the column entitled Snapper contains just the raw Snapper output excluding few false-positive motifs that were removed after manual results observation. The raw Snapper output and the verification process of this particular case are available in Supplementary Material S1. The PacBio results for H.pylori J99 were taken from the work of Krebes et al. (2014) directly (with few changes since the authors considered not the wild J99 strain but the J99-3 mutant). For Tombo, the best results that we managed to obtain with MEME are shown. For Nanodisco, the manually curated results are shown since the results generated in the automated mode were drastically less accurate.
These motifs were extracted as different because the algorithm is designed to be quite cautious in motifs merging to prevent occasional motif collisions.