CSC 334: Midterm Grading Rubric Part 1: (10pts) (a) 3 - choose the overlap with maximum length and no mismatches (b) 4 - correct de Bruijn graph (should have a loop) 2 - linear or otherwise incorrect de Bruijn graph (c) 3 - correct sequence and path 2 - minor mistake in sequence Part 2: (25pts) (a) 5 - correct explanation that links “0’s” and disallowing negative scores to being able to start and end a local alignment at any point 2 - explanation does not link local alignment to algorithm details (b) 10 - completely correct table and analysis of score(4,4) 2 - table is for global alignment instead (c) 5 - best alignment score of 3, correct two tracebacks, correct analysis of one of the alignments as a read overlap 3 - minor errors in alignments or analysis of read overlaps 1 - global alignments returned (d) 5 - correct 2 cases (last row to first col) or (last col to first row) 2 - partially correct (something about last/first row/col) Part 3: (10pts) 10 - correctly returns BWT of string (+2) - extra credit for correct reverse BWT (no partial credit) Part 4: (20pts) 10 - UPGMA correct with all branch lengths labeled 8 - few incorrect lengths and/or missing lengths 10 - NJ correct with all branch lengths labeled, and correctly identified as closer to the truth 8 - few incorrect lengths and/or missing lengths 2 - distances from the matrix labeled on the tree Part 5: (10pts) 10 - correct tree and all steps shown 8 - missing a step, leading to incorrect tree Part 6: (25pts) (a) 8 - Fitch correct and better solution correct (4 vs. 3 mutations) 5 - problem with better solution and/or mutations incorrect (b) 12 - algorithm will correctly minimize the number of mutations for any non-binary tree, with notation and explanation of each step 10 - right idea but minor problem (missing top-down step, etc) 6 - a valid algorithm but doesn’t minimize the number of mutations (c) 5 - algorithm works correctly on the example tree (root is C), 6 mutations 2 - algorithm run but doesn’t return the correct result