Agenda • Background • Needleman-Wunsch • GPU Implementation • Optimization steps • Results Symposium on Application Accelerators in High-Performance Computing 2 Roche 454 GS FLX Titanium XL+ Typical Throughput 700 Mb Run Time 23 hours Read Length Up to 1,000 bp Reads per Run ~1,000,000 shotgun Symposium on Application Accelerators in High-Performance Computing 3 From Genomics to Metagenomics Symposium on Application Accelerators in High-Performance Computing 4 Why AmpliconNoise? 454 Pyrosequencing in Metagenomics has no consensus sequences -------- Overestimation of the number of operational taxonomic units (OTUs)  C. Quince, A. Lanzn, T. Curtis, R. Davenport, N. Hall,I ...

 

Overview Southern-blot DNA Digestion Based hybridization COBRA MSP Bisulfite Sequencing Bisulfite Based Real-time MSP MethyLight MassARRAY Pyrosequencing Southern Blot Hybridization 1978 -One of the older techniques for sequencing (1978), not as widely used any more due to the development of PCR and other cheap/fast sequencing techniques, not outdated but just not as widely employed Process: • Step 1 use restriction enzymes to cut DNA • Step 2 electrophoresis to separate DNA fragments by size • Step 3 transfer DNA fragments from gel to a membrane • Step 4 hybridize radiolabeled probe to membrane • Step 5 sample is washed to ...