RAPID-2, an object-oriented associative memory applicable to genome data processing

We present on-going research concerning an object oriented associative memory. It is a massively parallel architecture, fully programmable and configurable, composed of VLSI circuits. It is well adapted to genome data processing. DNA and proteins sequences alignment is a very important application in biology research. Standard sequences alignment usually entails software implementation with disastrous execution time (typically one year). A parallel implementation can solve such a problem. Rapid-2 will be able to execute and accelerate genome tasks. We programmed and simulated several variants of the Needleman and Wunsch algorithm (1970) with progressive complexity (gaps, Dayhoff mutation matrix). Execution time evaluations of all these methods are presented. We consider that Rapid-2 could improve software implementation of a factor 100.<>