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Table 2 A comparison with CUDASW++ 2.0

From: DOPA: GPU-based protein alignment using database and memory access optimizations

No.

Optimizations

CUDASW++ 2.0

DOPA

(less optimized)

DOPA

(optimized)

1

Database sorting

+

+

+

2

Concatenation into sequence groups

-

+

+

3

Interlacing

+

+

+

4

Equal length sequence sets

-

-

+

5

Query profile

+

+

+

  1. The table compares the optimization steps adapted by DOPA and CUDASW++ 2.0.