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Table 2 Memory for neighborhood storage for different alphabets with adapted neighborhood lengths

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%

 
  1. for neighborhood storage is computed with respect to sensitivity/selectivity trade-offs shown on Figure 7.