This Small Business Technology Transfer (STTR) Phase I research project aims to develop a Field Programmable Gate Array (FPGA) based co-processing unit that will enable more rapid searches of protein and nucleic acid data by allowing, among other functions, one core of a multicore system to be used as a co-processing unit for data management. Enabling faster comparison and analysis of sequences is essential to the more efficient alignment and identification of molecules such as proteins and nucleic acids whose numbers have grown tremendously over the last two decades and continue to increase.
The efficient mining of various databases with tools that allow rapid regional and global alignments is an important part of bioinformatics. With the increasing complexity of the volume of protein and nucleic acid sequence data, it is imperative that hardware and software tools be developed that would allow fast searches of these growing databases. Production of a Field Programmable Gate Array based co-processing unit would enable such a computational acceleration and would improve the currently obtained speeds by a considerable margin. As such, the effects of the technology are likely to be significant.
