Searching Biological Sequence Databases Using Distributed Adaptive Computing

TR Number



Journal Title

Journal ISSN

Volume Title


Virginia Tech


Genetic research projects currently can require enormous computing power to processes the vast quantities of data available. Further, DNA sequencing projects are generating data at an exponential rate greater than that of the development microprocessor technology; thus, new, faster methods and techniques of processing this data are needed. One common type of processing involves searching a sequence database for the most similar sequences. Here we present a distributed database search system that utilizes adaptive computing technologies. The search is performed using the Smith-Waterman algorithm, a common sequence comparison algorithm. To reduce the total search time, an initial search is performed using a version of the algorithm, implemented in adaptive computing hardware, which is designed to efficiently perform the initial search. A final search is performed using a complete version of the algorithm. This two-stage search, employing adaptive and distributed hardware, achieves a performance increase of several orders of magnitude over similar processor based systems.



bioinformatics, Smith-Waterman algorithm, adaptive computing, configurable computing, sequence comparison, sequence alignment, Field programmable gate arrays