CAAD BLASTn: Accelerated NCBI BLASTn with FPGA prefiltering

Abstract

The canonical bioinformatics application is determining the biological similarity of a new sequence (protein or DNA) with respect to databases of known sequences. The BLAST algorithm is used for the vast majority of these searches. Of the various BLAST implementations, the one published by NCBI is a recognized standard. In previous work we described FPGA acceleration of the protein version of NCBI BLAST (BLASTp) using our TreeBLAST-based filter. Here we apply this filter to NCBI BLASTn, the DNA version. We show the modifications to the structures of the filtering components needed to handle DNA, as opposed to protein, sequences. The design has been implemented on an Altera Stratix III family chip. Our experimental results show that the speedup is greater than 12x and the accuracy is 100%. ©2010 IEEE.