PROTEIN SEQUENCE ALIGNMENT ANALYSIS USING GPU ACCELERATED BASED TOOLS FOR HUMAN GENOME.

Basic Local Alignment Search Tool (BLAST) is the program that finds regions of similarity between biological sequences (DNA, RNA and Protein). The program compares nucleotide or protein sequences to databases with sequences and calculates the statistical significance. It finds regions of local similarity between sequences. There are many types of BLAST present based on the query sequence input given. The protein-protein BLAST (blastp) is a program in which the given protein query returns the most similar protein sequences from the protein database when a user specifies. Most of the sequence similarity search runs on Central Processing Unit (CPU). A Graphics Processing Unit (GPU) is a specialized electronic circuit designed to rapidly manipulate and alter memory. It is occasionally called as Visual Processing Unit (VPU). It accelerates the creation of images in a frame buffer intended for output to a display. GPUs are used in mobile phones, personal computers, workstations, embedded systems, and game consoles. Modern GPUs are very efficient at manipulating computer graphics and image processing. Their highly parallel structure makes them more efficient than general-purpose CPUs for algorithms, where processing of large blocks of data is done in parallel. A GPU can be present on a video card in a personal computer. It can be embedded on the motherboard or in certain CPUs it is present on the CPU die. In the present work, the review of the GPU bases software analysis for sequence analysis was being discussed. Blastp Algorithm is being implemented for analysis of Human Protein Sequences. The DNA sequences were first analyzed using BLAST +2.2.28 and then analyzed using GPU BLAST and GPU softwares like BarraCUDA, CUSHAW, G-DNA and G-MSA. The interpreted results were obtained and compared from one another and also with CPU based BLAST programs.