CS 262 Discussion Section 1.ppt

CS 262 Discussion Section 1 Purpose of discussion sections To clarify difficulties/ambiguities in the problem set questions and lecture material. To supplement class material by going somewhat into the biological concepts and motivations underlying this field. To discuss more algorithms from a topic, wherever needed. Antiparallel vs Parallel strands The DNA strand has a chemical polarity The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel Prokaryotes do not have a nucleus, eukaryotes do Eukaryotic DNA is packaged into chromosomes A chromosome is a single, enormously long, linear DNA molecule associated with proteins that fold and pack the fine thread of DNA into a more compact structure. Human Genome: 3.2 x 109 base pairs distributed over 46 chromosomes. A display of the full set of 46 chromosomes Sequence similarity Biological motivation Sequence similarity is useful in hypothesizing the function of a new sequence… … assuming that sequence similarity implies structural and functional similarity. Case Study: Multiple Sclerosis Multiple sclerosis is an autoimmune dysfunction in which the T-cells of the immune system start attacking the body’s own nerve cells. The T-cells recognize the myelin sheath protein of neurons as foreign. Show movie Why does this happen? A hypothesis: Possibly, the myelin sheath proteins identified by the T-cells were similar to bacterial/viral sheath proteins from an earlier infection. How to test this hypothesis? Use sequence alignment. Dynamic Programming It is a way of solving problems (involving recurrence relations) by storing partial results. Consider the Fibonacci Series: F(n) = F(n-1) + F(n-2) F(0) = 0, F(1) = 1 A recursive algorithm will take exponential time to find F(n) A Dynamic Prog. based solution takes only n steps (linear time) Needleman-Wunsch algorithm F(i,j) = Maximum of F(i-1, j-1) + s(x[i], y[j]) F(i-1, j) – d F(i, j-1) - d Needleman-Wunsch examp