Advances in genomics, proteomics, and bioinformatics have revolutionized the drug discovery and drug development. Computational systems biology, computational bioinformatics, and many biomedical applications are also growing at a rapid pace with an increasing demand for processing power. Hardware clusters and grid computing solutions are approached to fulfill the high demand for the processing power. The grid clusters approach proved success but introduced the need of frameworks to hide the complexity of parallel programming and enable the programmer to focus on the application logic. In this paper we present a novel cloud computing based neural network framework. We will further present results of implementation of Multiple Sequence Alignment (MSA) algorithms in cloud architecture. The experiments show optimal results in terms of computational complexity and preserve accuracy as well.