Bioinformatic searches using a single-chip shared-memory multiprocessor

摘要

A single-chip shared-memory multiprocessor architecture is introduced which is particularly well suited to common bioin-formatic computing tasks. The architecture uses asynchronous bus interfaces to create an integrated circuit design methodology allowing for scaling of the multiprocessor with very little design effort. A key aspect of this design methodology is that it is not necessary to expend significant design resources and chip area on the clock tree. An analysis of the Smith-Waterman alignment algorithm running on this architecture shows that the performance penalty due to increased bus latency compared to a fully synchronous architecture is negligible.