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Table 8 Practical results for different alphabets – Quality estimations

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

  1. Similarity search results obtained on reduced alphabets. The number of positions tested (validating Stage 1 only and independent from the chosen alphabet) is 1.59 * 109. The practical selectivity is computed dividing the number of positions validating both Stage 1 and Stage 2 by the number of positions tested.