Development of technologies in bioinformatics resulted into many folds growth of biological data that led to the research for accelerated solutions in various domains of computational bioinformatics. String matching is one of the most widely performed tasks at various stages of computational pipeline and it needs an accelerated and reconfigurable methodology for implementation. In this paper we present hardware-software codesign based accelerated and reconfigurable methodology for string matching and verify it using protein identification as a case study. In addition to real-time reconfigurability, our proposed methodology for string matching is 4 and 1.5 times faster than state of the art software and hardware methods respectively. © 2017 IEEE.