A Graphics Processing Unit Based Multi-String Matching Algorithm
String matching is a fundamental problem in computer science. It plays an important role in search engine, virus detection, sequence alignment and many other applications. Aho-Corasick (AC) algorithm is a widely used multi-string matching algorithm. In this paper, we present a space compacting method for AC automata based on node grouping and implement AC algorithm on GPU platform using CUDA (Computer Unified Device Architecture). In several experiments we conduct, our multi-string algorithm archives at least 10 times of speedup of the algorithm on CPUs.
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Document Type: Research Article
Publication date: August 1, 2013
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- Bionanoscience attempts to harness various functions of biological macromolecules and integrate them with engineering for technological applications. It is based on a bottom-up approach and encompasses structural biology, biomacromolecular engineering, material science, and engineering, extending the horizon of material science. The journal aims at publication of (i) Letters (ii) Reviews (3) Concepts (4) Rapid communications (5) Research papers (6) Book reviews (7) Conference announcements in the interface between chemistry, physics, biology, material science, and technology. The use of biological macromolecules as sensors, biomaterials, information storage devices, biomolecular arrays, molecular machines is significantly increasing. The traditional disciplines of chemistry, physics, and biology are overlapping and coalescing with nanoscale science and technology. Currently research in this area is scattered in different journals and this journal seeks to bring them under a single umbrella to ensure highest quality peer-reviewed research for rapid dissemination in areas that are in the forefront of science and technology which is witnessing phenomenal and accelerated growth.
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