A Highly Efficient Substitution Matrix Loader for Pairwise Sequence Alignment

This paper presents a novel substitution matrix loader architecture for pairwise sequence alignment. The search for sequence homology using DP-based alignment matrix computation is an important tool in molecular biology. It can be implemented either by optimal or sub-optimal approaches. Both of these methods require frequent and rapid access to the amino acids probability scores for PE (Processing Element) configuration especially in a folded systolic array. Typical FPGA implementations configure look-up tables in the pipeline PEs either by using a serial configuration chain with different look-up tables or by run time reconfiguration of the same look-up table. In the former case, configuration time increases proportionally to the number of look-up tables, while the latter case suffers from the limited reconfiguration bandwidth. Therefore, in this paper, we propose a highly efficient parallel loader to optimize both time and space complexities of protein sequence alignment in folded systolic arrays, using only two configuration elements (CEs). In addition, the proposed loader enables PEs to be updated with substitution matrix scores concurrently, with the worst case configuration time of 2 x the depth of the PE's look-up table (in clock cycles). This allows for further optimization of the most time consuming alignment matrix computation through efficient scheduling of alignment matrix computation and PE configuration. Implementation results show that the proposed architecture achieves k.N-PE speed-up in configuration time (where k is the folding factor and N-PE is the number of PEs) compared to classical approaches, at virtually no area overhead.