BINF 5445 HW 8 due M 10/27/08

1. Note the tool ORF Finder (mentioned on p. 119 of Westhead). Try it out. Hand in the relevant screens and explanations in hard copy.
2. What is the most similar exercise or example to the preceding problem that you can design based on the new book?
3. Consider measuring the quality of a gene finder system. See p. 120 of Westhead.
1. Using figures from another hypothetical gene finder system of 40 predicted positives, 60 predicted negatives, 36 actual positives, 64 actual negatives, 32 true positives, 56 true negatives, 8 false positives, and 4 false negatives, calculate its sensitivity and specificity.
2. Using figures from a hypothetical gene finder system of 100 false positives, 200 false negatives, 300 true positives, and 400 true negatives, calculate its sensitivity and specificity.
3. Explain if the new book gives enough explanation to enable someone to solve parts A and B, or if one really needs Westhead to do it.
4. The last paragraph on p. 120 gives some numbers for the best available systems. Is it possible to compute the AC given those numbers? If so, do it. Does the new book give analogous sample numbers?