The Reconfigurable Hardware Accelerator for Searching Genome Patterns

The presented work concerns application of modern, complex programmable hardware devices in computation biology. The Xilinx Virtex 5 with PCI-Express interface has been used to implement the searching algorithm based on the dynamic programming idea. This algorithm works on very long chains of symbols, which come from reference pattern of the genome and we try to find some query sequences within those chains. The software solutions in the field are very limited and they need large time and space resources, so we have decided to implement the entire system on the reconfigurable hardware platform. We have investigated some variants of the implementation taking into account available resources, properties of the hardware and possibilities of parallel processing and increasing the overall system performance. The results we have obtained are very promising and show the dominance of the dedicated platforms over the general purpose PC-based systems.