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Accelerated Profile HMM Searches

Figure 2

Illustration of striped indexing for SIMD vector calculations.

The top row (magenta outline) shows one row of the dynamic programming lattice for a model of length . Assuming an example of vectors containing cells each, the 14 cells are contained in vectors numbered . (Two unused cells, marked x, are set to a sentinel value.) In the dynamic programming recursion, when we calculate each new cell in a new row , we access the value in cell in the previous row . With striped indexing, vector contains exactly the four cells needed to calculate the four cells in a new vector on a new row of the dynamic programming matrix (turquoise outline). For example, when we calculate cells in vector , we access the previous row's vector which contains the cells we need in the order we need them, (dashed lines and box). If instead we indexed cells into vectors in the obvious way, in linear order ( in vector and so on), there is no such correspondence of with four 's, and each calculation of a new vector would require expensive meddling with the order of cells in the previous row's vectors. With striped indexing, only one shift operation is needed per row, outside the innermost loop: the last vector on each finished row is rightshifted (mpv, in grey with red cell indices) and used to initialize the next row calculation.

doi: https://doi.org/10.1371/journal.pcbi.1002195.g002