Sequence alignment algorithms are a key component of many bioinformatics applications. The NCBI BLAST [1, 2] is a widely used tool that implements algorithms for sequence comparison. These algorithms are the basis for many other types of BLAST searches such as BLASTX, TBLASTN, and BLASTP . The demand for processing large amounts of genomic data that gushes from NGS devices has grown faster than the rate which industry can increase the power of computers (known as Moore’s Law). This fact has raised new challenges for the implementation of scalable and efficient computational systems. In this scenario, MapReduce (and its Hadoop implementation) emerged as a paramount framework that supports design patterns which represent general reusable solutions to commonly occurring problems across a variety of problem domains including analysis and assembly of biological sequences . MapReduce has delivered outstanding performance and scalability for a myriad of applications running over hundreds to thousands of processing nodes . On the other hand, over the last decade, cloud computing has emerged as a powerful platform for the agile and dynamic provisioning of computational resources for computational and data intensive problems.