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Recently, many new next-generation sequencing techniques have been proposed. These techniques can produce lot of short reads rapidly. Hence, a number of tools have been developed to map these short reads to the genome. However, with more and more reads sequenced and the length of reads increases, these tools require high memory usage and huge computational cost and are also impractical for utilization...
Regular expression (Regex) becomes the standard signature language for security and application detection. Deterministic finite automata (DFAs) are widely used to perform regex matching in linear time. Previously researches mostly focus on how to compress DFA to reduce memory requirements in recent years. However, memory requirement is not the only problem caused by DFA explosion when implementation...
Multi-string matching is a key technique for implementing network security applications like Network Intrusion Detection Systems (NIDS). Existing DFA-based approaches always tradeoff between memory and throughput, and fail to has the best of both worlds. This paper extends the classic longest prefix principle from single-character to multi-character string matching and proposes a multi-string matching...
After the reference genomes of many organisms are sequenced in this post-genetic era, it has become an extremely important issue that how to do the re-sequencing and assembly for individual genomes from very large amount of reads. In this paper, we will present a re-sequencing tool designed for the Next Generation Sequencing (NGS) data. And these data are composed of a huge amount of short reads which...
Multi-string matching is a key technique for network security applications like Network Intrusion Detection Systems (NIDS) and anti-virus scanners. %, where every packet is inspected against thousands of predefined signatures in real time. Existing DFA-based approaches always tradeoff between memory and throughput, no known approach has the best of both worlds. Hence, they fail to be used in the embedded...
Deep packet inspection at high speed has become extremely important due to its application in a wide range of network applications, such as network security and network monitoring. Network intrusion detection system (NIDS) uses a collection of signatures of known security threats and viruses to scan the payload of each packet. Signatures are often specified in the form of regular expressions (regex),...
New applications such as real-time deep packet inspection require high-speed regular expression (regex) matcher, and the number of regexes in pattern store is increasing to several thousands, which requires a memory efficient solution. In this paper, a kind of hardware based compact DFA structure for multiple regexes matching called CPDFA is presented. According to statistics of regexes in Snort and...
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