From: Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER
Data structure | COPS (proposed) | ViterbiFilter |
---|---|---|
(HMMER) | ||
Mmx, Dmx, Imx | 3×M×16 | 3×M×2 |
Transition scores | 8×M×16 | 8×M×2 |
Emission match (E.M.) scores | M×16 | M×2 |
Auxiliary emission array | 24×16 | – |
∼20 aux. variables | 20×16 | 20×16 |
Total | 192×M+700 | 24×M+320 |
Total minus E.M. scores | 176×M+700 | 22×M+320 |
Max. M to fill a 32 KB cache |
|
|