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A hardware accelerator for the alignment of multiple DNA sequences in forensic identification

The comparison of DNA sequences is a classic problem in molecular biology. Forensic applications uses this comparison for personal identication. For instance, in the USA, the CODIS system has today 14.9 million DNA proles stored on its database. To accelerate the recurrent task to query into similar databases, this work presents a hardware acderator for the parallel alignment of multiple DNA sequences, aiming for the maximum throughput Each of these alignments is done using the Needleman-Wunsch algorithm which represents an optimal global technique for measuring the similarity between DNA sequences. The proposed accelerator architecture optimizes the use of hardware resources, the data access strategy and, as a result, memory bandwidth. The experiments were conducted using a synthetic DNA database with 8 million individuals, in which, each of them is represented using a set of 15 sequences with a length of 240 nucleotides. In this case study, a prototype of the proposed hardware accelerator using a single Stratix IV FPGA is running at the frequency of 280MHz and outperforms by tens of times consolidated software applications like SWIPE and FASTA which are running in a high performance GPP platform, as well as optimized GPU implementation in OpenCL.