Sequence alignment is the fundamental operation in molecular biology for comparing bio molecular sequences to identify regions of similarity that consequences of structural, functional, or evolutionary relationships. ClustalW is a progressive alignment algorithm for multiple sequence alignment.
- Step 1: Determine all pairwise alignment between sequences and determine degrees of similarity between each pair.
- Step 2: Construct a guide tree.
- Step 3: Combine the alignments starting from the most closely related groups to the most distantly related groups, using the “once a gap always a gap” rule.
Graphics Processor Unit (GPU) are general purpose stream processor capable of very high computation and data throughput. In certain applications requiring massive vector operations, this can yield several orders of magnitude higher performance than a conventional CPU.
This work comprises of parallel implementation of ClustalW algorithm using CUDA. The resulting implementation design has to be optimized in terms of throughput and latency requirements.
Prerequisites: C programming.
Prerequisites: C programming.
Contact: Muhammad Kashif Hanif
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