A novel algorithm for online inexact string matching and its FPGA implementation

TL;DR

This paper presents a new online approximate string matching algorithm that filters shadow hits in real-time and demonstrates its efficient FPGA hardware implementation, outperforming software solutions in speed and cost.

Contribution

The paper introduces a novel online approximate string matching algorithm with real-time filtering capabilities and provides an FPGA implementation that enhances performance and cost-efficiency.

Findings

FPGA implementation achieves high parallelism and speed.

Algorithm effectively filters shadow hits on the fly.

Hardware design maintains low logic element usage.

Abstract

Accelerating inexact string matching procedures is of utmost importance when dealing with practical applications where huge amount of data must be processed in real time, as usual in bioinformatics or cybersecurity. Inexact matching procedures can yield multiple shadow hits, which must be filtered, according to some criterion, to obtain a concise and meaningful list of occurrences. The filtering procedures are often computationally demanding and are performed offline in a post-processing phase. This paper introduces a novel algorithm for Online Approximate String Matching (OASM) able to filter shadow hits on the fly, according to general purpose priority rules that greedily assign priorities to overlapping hits. An FPGA hardware implementation of OASM is proposed and compared with a serial software version. Even when implemented on entry level FPGAs, the proposed procedure can reach a high degree of parallelism and superior performance in time compared to the software implementation, while keeping low the usage of logic elements. This makes the developed architecture very competitive in terms of both performance and cost of the overall computing system.