I am a bioinformatics graduate student looking to do a short project using CUDA. I would like compare the performance of simple bioinformatics algorithms executing on either the CPU or GPU. Thus, for each selected algorithm, I would code one version in C and another using CUDA. Execution times would then be compared and analyzed.
I am wondering if anyone can suggest some simple algorithms or program ideas that might lend themselves to parallel computation. I am thinking about very simple problems...an example might be sequence alignment...
I do have a good amount of programming experience and have used CUDA for about a month now.
Any help would be appreciated and Thank You!