Scalability of Bioinformatics Applications for Multicore Architectures

Exponential growth in biological sequence data combined with the computationally intensive nature of bioinformatics applications results in a continuously rising demand for processing power. Microprocessor complexity and, more importantly, computational capability increases as well, through transistor budgets that grow in line with Moore's law....

An Efficient and High Performance Linear Recursive Variable Expansion Implementation of the Smith-Waterman Algorithm

In this paper, we present an efficient and high performance linear recursive variable expansion (RVE) implementation of the Smith-Waterman (S-W) algorithm and compare it with a traditional linear systolic array implementation. The results demonstrate that the linear RVE implementation performs up to 2.33 times better than the traditional linear...

Development of a workload set for multi-core architectures

With the rise of multi-core chips in commodity hardware, the need for specialized workloads to evaluate the performance of multi-core systems has become apparent. The current generation of workloads used for evaluating multi-core systems often consist of sequential programs not capable of running on multiple processors and are therefore of...