%0 Journal Article %A M. Bakhouya and S. A. Bahra and T. El-Ghazawi %D 2008 %J International Journal of Electrical and Computer Engineering %B World Academy of Science, Engineering and Technology %I Open Science Index 14, 2008 %T Using the PGAS Programming Paradigm for Biological Sequence Alignment on a Chip Multi-Threading Architecture %U https://publications.waset.org/pdf/12329 %V 14 %X The Partitioned Global Address Space (PGAS) programming paradigm offers ease-of-use in expressing parallelism through a global shared address space while emphasizing performance by providing locality awareness through the partitioning of this address space. Therefore, the interest in PGAS programming languages is growing and many new languages have emerged and are becoming ubiquitously available on nearly all modern parallel architectures. Recently, new parallel machines with multiple cores are designed for targeting high performance applications. Most of the efforts have gone into benchmarking but there are a few examples of real high performance applications running on multicore machines. In this paper, we present and evaluate a parallelization technique for implementing a local DNA sequence alignment algorithm using a PGAS based language, UPC (Unified Parallel C) on a chip multithreading architecture, the UltraSPARC T1. %P 296 - 300