CAAD BLASTP: NCBI BLASTP Accelerated with FPGA-Based Pre-Filtering

NCBI BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. The problem is that it uses complex heuristics which make it difficult to simultaneously achieve both substantial speed-up and exact agreement with the original output. Our approach is to prefilter the database. To make this work we have developed a novel heuristic which we append to a previously described structure for ungapped alignment. This enables us to quickly reduce the database by factors of 300 and 1100, for the ungapped and gapped options, respectively, while rejecting no significant sequences. On current hardware we anticipate a speed-up of at least a factor of 10 for NCBI BLASTP, independent of sensitivity settings. This filter is portable to other BLAST codes, and other filters can be similarly integrated into NCBI BLAST.