From: Optimal neighborhood indexing for protein similarity search
indexed neighborhood alphabet | bits per character (α) | neighborhoods length (L) | total per index line (2αL) | relative gain compared to Σ20 (1 – 2αL/ 110) | |
---|---|---|---|---|---|
Σ20 | 5 | 11 | 110 | 0% | Memory |
Σ16 | 4 | 12 | 96 | 13% | |
Σ8 | 3 | 14 | 84 | 24% | |
Σ4 | 2 | 19 | 76 | 31% | |
Σ2 | 1 | 32 | 64 | 42% |