Bioinformatics is one of the interdisciplinary research area. In various genome projects, huge biological sequences are available. Biological sequence analysis is fundamental operation in Bioinformatics and the goal is to find the similarity region based on comparing method is called as sequence alignment. In sequences alignment two methods are reported that are local alignment and global alignment. Smith-Waterman (SW) algorithm is providing optimal local alignment which has quadratic time and space complexity. In several real time applications huge sequences are aligned. In ordered to increase the efficiency, biological sequences are aligned over Graphical Processing Unit (GPU). Various systems applies parallel algorithm with use of GPU to accelerate application. CUDA Align algorithm is used to obtain full optimal alignment of biological sequences and the idea behind this is to obtain coordinate point of optimal alignment, iteratively perform same process to increase number of coordin