From: Optimal neighborhood indexing for protein similarity search
alphabets | number of positions validating Stage 1 and Stage 2 | practical selectivity | number of detected alignments | practical sensitivity |
---|---|---|---|---|
Σ20 × Σ20 | 2.14 * 106 | 1.35 * 10-3 | 650 (all) | 1 |
Σ20 × Σ16 | 1.39 * 106 | 0.88 * 10-3 | 650 (all) | 1 |
Σ20 × Σ16 | 0.98 * 106 | 0.62 * 10-3 | 650 (all) | 1 |
Σ20 × Σ8 | 0.62 * 106 | 0.39 * 10-3 | 650 (all) | 1 |
Σ20 × Σ4 | 3.14 * 106 | 1.98 * 10-3 | 650 (all) | 1 |
Σ20 × Σ2 | 2.93 * 106 | 1.85 * 10-3 | 650 (all) | 1 |