SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

BACKGROUND The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not...

Parleda: a Library for Parallel Processing in Computational Geometry Applications

ParLeda is a software library that provides the basic primitives needed for parallel implementation of computational geometry applications. It can also be used in implementing a parallel application that uses geometric data structures. The parallel model that we use is based on a new heterogeneous parallel model named HBSP, which is based on BSP and is introduced here. ParLeda uses two main lib...

EVE, an Object Oriented SIMD Library

This paper describes the eve (Expressive Velocity Engine) library, an object oriented C++ library designed to ease the process of writting efficient numerical applications using AltiVec, the SIMD extension designed by Apple, Motorola and IBM. AltiVec-powered applications typically show off a relative speed up of 4 to 16 but need a complex and awkward programmation style. By using various templa...

Margaret Chase Smith library

GPU Accelerated Smith-Waterman

We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonst...