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Table 1 Memory footprint (in Bytes) required by the proposed COPS implementation, when compared with the original HMMER ViterbyFilter

From: Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER

Data structure

COPS (proposed)

ViterbiFilter

  

(HMMER)

Mmx, Dmx, Imx

M×16

M×2

Transition scores

M×16

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

32768 - 700 192 167

32768 - 320 24 1350

  1. M represents the model length and all the computed scores are represented with 16-bit integers.