During the last years computer science has taken on an increasingly central role in the processes underlying the production and analysis of biological data. The continuous development of new cutting-edge machines such as NGS has made it possible to make great progress in the field of genetic sequence analysis. For this reason, and also due to the enormous amount of data produced daily with these procedures, many algorithms and tools developed for the analysis need to be optimized for exploiting the enhanced features of new computing systems. With this thesis work I propose a modern reimplementation of an alignment tool called isomiR-SEA which was developed with a precise objective in mind: overcoming some of the limitations of today’s general-purpose alignment algorithms, that usually lack accuracy and completeness in the results.