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Rahul Shirude, Valmik B. Nikam, B.B. Meshram
Bioinformatics is the field of science which applies computer science and information technology to the problems of biological science. One of the most useful applications of bioinformatics is sequence analysis. Sequence analysis, which is the process of subjecting a DNA, RNA to any wide range of analytical approaches, involves methodologies like sequence alignment and searches […]
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Nagaveni V, G T Raju
The main aim of string matching algorithm is to locate the appearance of a specific pattern in an array of larger size text. String matching algorithms has been used in many applications such as DNA analysis. This report introduces a new approach of string matching algorithm to detect the occurrence of several gene patterns in […]
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Cary Yang, Kevin Zhang
In this paper, we explore approaches to parallelizing the edit distance problem and the related approximate string matching problem. The edit distance is a measure of the number of individual character insertions, deletions, and substitutions requried to transform one string into another string. In the canonical dynamic programming solution to the edit distance, a chain […]
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Sanguthevar Rajasekaran, Lance Fiondella, Mohamed Ahmed, Reda A. Ammar
Every area of science and engineering today has to process voluminous data sets. Using exact, or even approximate, algorithms to solve intractable problems in critical areas, such as computational biology, takes time that is exponential in some of the underlying parameters. Parallel computing addresses this issue and has become affordable with the advent of multicore […]
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Adnan Ozsoy, Martin Swany, Arun Chauhan
In this paper, we present an algorithm and provide design improvements needed to port the serial Lempel-Ziv-Storer-Szymanski (LZSS), lossless data compression algorithm, to a parallelized version suitable for general purpose graphic processor units (GPGPU), specifically for NVIDIA’s CUDA Framework. The two main stages of the algorithm, substring matching and encoding, are studied in detail to […]
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Kazumasa Ikeuchi, Janaka Wijekoon, Shinichi Ishida, Hiroaki Nishi
Service-oriented router (SoR) is a new router architecture for providing rich services to Internet users by utilizing useful information extracted from network traffic. In SoR, stream reconstruction and selection is a fundamental process for providing the services in the application layer. After real-time reconstruction of stream data, SoR used a software character string analyzer to […]
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Charalampos S. Kouzinopoulos
String matching is a fundamental problem in the area of scientific computing. When two different one-dimensional strings are taken as an input, the so called "input string" and the so called "pattern", the string matching problem involves the location of all the positions in the input string where the pattern appears. As there has been […]
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Hirohito Sasakawa, Hiroki Arimura
In this paper, we propose fast string matching system using GPU for large scale string matching. The key of our proposed system is the use of bit-parallel pattern matching approach for compact NFA representation and fast simulation of NFA transition on GPU. In the experiments, we show the usefulness of our proposed pattern matching system.
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Saima Haseeb, Mahak Motwani, Amit Saxena
With the rapid growth of Internet, E-mail, with its convenient and efficient characteristics, has become an important means of communication in people’s life. It reduces the cost of communication. It comes with Spam. Spam emails, also known as "junk e-mails", are unsolicited one’s sent in bulk with hidden or forged identity of the sender, address, […]
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Weibin Sun, Robert Ricci
We introduce Snap, a framework for packet processing that outperforms traditional software routers by exploiting the parallelism available on modern GPUs. While obtaining high performance, it remains extremely flexible, with packet-processing tasks implemented as simple modular elements that are composed to build fully functional routers and switches. Snap is based on the Click modular router, […]
Ong Wen Mei
Since the last decade, the concept of general purpose computing on graphics processors was introduced and has since garnered significant adaptation in the engineering industry. The use of a Graphics Processing Unit (GPU) as a many-core processing architecture for the purpose of general-purpose computation yields performance improvement of several orders-of magnitude. One example in leveraging […]
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X. Bellekens, I. Andonovic, RC. Atkinson
Graphics Processing Units (GPUs) have become the focus of much interest with the scientific community lately due to their highly parallel computing capabilities, and cost effectiveness. They have evolved from simple graphic rendering devices to extremely complex parallel processors, used in a plethora of scientific areas. This paper outlines experimental results of a comparison between […]
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