Hardware software co-design of the Aho-Corasick algorithm: Scalable for protein identification?

Pattern matching is commonly required in many application areas and bioinformatics is a major area of interest that requires both exact and approximate pattern matching. Much work has been done in this area, yet there is still a significant space for improvement in efficiency, flexibility, and throughput. This paper presents a hardware software co-design of Aho-Corasick algorithm in Nios II soft-processor and a study on its scalability for a pattern matching application. A software only approach is used to compare the throughput and the scalability of the hardware software co-design approach. According to the results we obtained, we conclude that the hardware software co-design implementation shows a maximum of 10 times speed up for pattern size of 1200 peptides compared to the software only implementation. The results also show that the hardware software co-design approach scales well for increasing data size compared to the software only approach

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists

FPGA acceleration of DNA sequence alignment: design analysis and optimization

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. In this work, we propose a runtime reconfigurable alignment pipeline that considers all information in sequencing data for the biologically accurate acceleration of short read mapping. We focus our efforts on accelerating two string matching techniques: FM-index and the Smith-Waterman algorithm with the affine-gap model which are commonly used in short read mapping. We further optimize the FPGA hardware using a design analyzer and merger to improve alignment performance. The contributions of this work are as follows. 1. We accelerate the exact-match and mismatch alignment by leveraging the FM-index technique. We optimize memory access by compressing the data structure and interleaving the access with multiple short reads. The FM-index hardware also considers complete information in the read data to maximize accuracy. 2. We propose a seed-and-extend model to accelerate alignment with indels. The FM-index hardware is extended to support the seeding stage while a Smith-Waterman implementation with the affine-gap model is developed on FPGA for the extension stage. This model can improve the efficiency of indel alignment with comparable accuracy versus state-of-the-art software. 3. We present an approach for merging multiple FPGA designs into a single hardware design, so that multiple place-and-route tasks can be replaced by a single task to speed up functional evaluation of designs. We first experiment with this approach to demonstrate its feasibility for different designs. Then we apply this approach to optimize one of the proposed FPGA aligners for better alignment performance.Open Acces

Packet Inspection on Programmable Hardware

In the network security system, one of the issues that are being discussed is to conduct a quick inspection of all incoming and outgoing packet. In this paper, we make a design packet inspection systems using programmable hardware. We propose the packet inspection system using a Field Programmable Gate Array (FPGA). The system proposed consisting of two important parts. The first part is to scanning packet very fast and the second is for verifying the results of scanning the first part. On the first part, the system based on incoming packet contents, the packet can reduce the number of strings to be matched for each packet and, accordingly, feed the packet to a verifier in the second part to conduct accurate string matching. In this paper a novel multi-threading finite state machine is proposed, which improves the clock frequency and allows multiple packets to be examined by a single state machine simultaneously. Design techniques for high-speed interconnect and interface circuits are also presented. The results of our experiment show that the system performance depend on the string matching algorithm, design on FPGA, and the number of string to be matched. Keywords: Packet inspection, string matching, Field programmable gate array, Traffic classificatio

A Frame Work for Parallel String Matching- A Computational Approach with Omega Model

Now a day2019;s parallel string matching problem is attracted by so many researchers because of the importance in information retrieval systems. While it is very easily stated and many of the simple algorithms perform very well in practice, numerous works have been published on the subject and research is still very active. In this paper we propose a omega parallel computing model for parallel string matching. Experimental results show that, on a multi-processor system, the omega model implementation of the proposed parallel string matching algorithm can reduce string matching time by more than 40%

String Matching Problems with Parallel Approaches An Evaluation for the Most Recent Studies

In recent years string matching plays a functional role in many application like information retrieval, gene analysis, pattern recognition, linguistics, bioinformatics etc. For understanding the functional requirements of string matching algorithms, we surveyed the real time parallel string matching patterns to handle the current trends. Primarily, in this paper, we focus on present developments of parallel string matching, and the central ideas of the algorithms and their complexities. We present the performance of the different algorithms and their effectiveness. Finally this analysis helps the researchers to develop the better techniques