Table 2 Summary of comparison on results between global alignment, local alignment without gap penalty and local alignment with affine gap penalty when using the smallest threshold such that there is no false positive.
From: Local structural alignment of RNA with affine gap model
Family | Number of members | Number of misses | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Gotohscan [8] | % | Â | Global [10] | % | Â | Local | % | Â | Local with affine gap | % |
RF00014 | 96 | 2 | 2.1% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00021 | 100 | 10 | 10% | Â | 5 | 5% | Â | 5 | 5% | Â | 2 | 2% |
RF00022 | 100 | 59 | 59% | Â | 20 | 20% | Â | 19 | 19% | Â | 4 | 4% |
RF00027 | 100 | 100 | 100% | Â | 15 | 15% | Â | 9 | 9% | Â | 2 | 2% |
RF00032 | 100 | 59 | 59% | Â | 4 | 4% | Â | 1 | 1% | Â | 0 | 0% |
RF00033 | 100 | 29 | 29% | Â | 27 | 27% | Â | 27 | 27% | Â | 25 | 25% |
RF00034 | 100 | 71 | 71% | Â | 11 | 11% | Â | 22 | 22% | Â | 7 | 7% |
RF00038 | 100 | 88 | 88% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00039 | 100 | 100 | 100% | Â | 1 | 1% | Â | 1 | 1% | Â | 1 | 1% |
RF00042 | 100 | 10 | 10% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00043 | 21 | 3 | 14.3% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00044 | 8 | 1 | 12.5% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00046 | 76 | 9 | 11.8% | Â | 2 | 2.6% | Â | 1 | 1.3% | Â | 0 | 0% |
RF00048 | 100 | 17 | 17% | Â | 0 | 0% | Â | 0 | 0% | Â | 0 | 0% |
RF00386 | 100 | 88 | 88% | Â | 63 | 63% | Â | 62 | 62% | Â | 6 | 6% |
RF00643 | 100 | 98 | 98% | Â | 4 | 4% | Â | 13 | 13% | Â | 0 | 0% |
RF00661 | 100 | 100 | 100% | Â | 87 | 87% | Â | 77 | 77% | Â | 30 | 30% |
RF01051 | 100 | 100 | 100% | Â | 91 | 91% | Â | 85 | 85% | Â | 52 | 52% |
| Â | Â | average | 53.9% | Â | Â | 18.4% | Â | Â | 17.9% | Â | Â | 7.2% |