Fig. 3
From: HH-suite3 for fast remote homology detection and deep protein annotation
The layout of the log transition probabilities (top) and emission probabilities (bottom) in memory for single-instruction single data (SISD) and SIMD algorithms. For the SIMD algorithm, 4 (using SSE2) or 8 (using AVX 2) target profile HMMs (t1 – t4) are stored together in interleaved fashion: the 4 or 8 transition or emission values at position i in these HMMs are stored consecutively (indicated by the same color). In this way, a single cache line read of 64 bytes can fill four SSE2 or two AVX2 SIMD registers with 4 or 8 values each