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Table 1 Experimental machine

From: Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences

Item

Specification

CPU

Intel Xeon CPU E5-2680 v2 @ 2.80 GHz

Main memory

DDR3 512 GB

GPU

NVIDIA Tesla K40 ×2

Video memory

GDDR5 12 GB ×2

OS

Ubuntu 14.04.1

Compiler

gcc 4.8.2

Compiler option

O3

CUDA

CUDA 6.5