Agenda • Background • Next Generation Sequencing • Sequence Assembly • Sequence Alignment • Traditional Alignment Algorithms • Next Generation Alignment Algorithms • Conclusion Andy Nagar 2 Background • Earlier sequencing methods were based on Sanger sequencing, which goes back to the 1970s. • Sequencing was slow, bases were read one at a time. • Separation is done by electrophoresis. • Readout by fluorescent tags. Andy Nagar 3 Source:[Wikipedia] Background • To complete second generation genome projects such as the Human Genome Project, need for faster and high-throughput sequencing. • Next-Generation Sequencing technologies based on various implementations of cyclic array ...
Need to Add to part 2 or 3 A. Chip-seq B. Deep sequencing for expression profiling C. Illumina? movie Genomics Summary A. Microarrays: expression profiling and other uses B. Global Gene Knockouts C. Global protein localization in yeast D. Global complex identification in yeast E. Global two-hybrid analysis in yeast and other organisms F. RNAi G. Transgenics, gene “knock-outs” (genetics not genomics) H. Human Genome Project, Next Generation Sequencing, and Comparative Genomics Yeast “Knockout” Library Delete YFG Delete all genes (individually) Disruption of “All” Yeast Genes • Approx 6000 genes • Make 6000 sets of disruption primers ...
Next-Generation Sequencing y r o t a r o b ay Lt i ss er ce nv ei in cU S lg an nu oo iY t a tm ua ph mg oi r CB Problem Statement y r o t a r o •Map next-generation sequence reads b a y L t i with variable nucleotide confidence to s s e r c e n v e i a model reference genome that may i n c U S l g be different from the subject genome. a n n u o o i Y t a Speed ...
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