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Accelerating inexact string matching procedures is of utmost importance whendealing with practical applications where huge amount of data must be processedin real time, as usual in bioinformatics or cybersecurity. Inexact matchingprocedures can yield multiple shadow hits, which must be filtered, according tosome criterion, to obtain a concise and meaningful list of occurrences. Thefiltering procedures are often computationally demanding and are performedoffline in a post-processing phase. This paper introduces a novel algorithm forOnline Approximate String Matching (OASM) able to filter shadow hits on thefly, according to general purpose priority rules that greedily assignpriorities to overlapping hits. An FPGA hardware implementation of OASM isproposed and compared with a serial software version. Even when implemented onentry level FPGAs, the proposed procedure can reach a high degree ofparallelism and superior performance in time compared to the softwareimplementation, while keeping low the usage of logic elements. This makes thedeveloped architecture very competitive in terms of both performance and costof the overall computing system.

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