A reconfigurable architecture for scanning biosequence databases

Unknown protein sequences are often compared to a set of known sequences (a database scan) to detect functional similarities. Even though efficient dynamic programming algorithms exist for this problem, the required scanning time is still very high. The scan time requirements are likely to become even more severe because of the rapid growth in size of these databases. Thus, finding fast solutions is of high importance to research in this area. We present a new approach to biosequence database scanning using reconfigurable FPGA-based hardware platforms to gain high performance at low cost. To derive an efficient mapping onto this type of architecture, we have designed fine-grained parallel processing elements (PEs) that are tailored towards the parameters of a query. This results in an implementation with significant runtime savings on a standard FPGA.