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Unformatted text preview: BCB 567/CprE 548 Bioinformatics I Fall 2007 Exam 1 Solutions General Grading Principles: If for any question on the exam, you wrote down a statement that is not true for a problem, you were docked half a point for that problem. Equivalent solutions have been given equivalent number of points. 1. (a) The best local alignment is: CC-GA CCAGA (b) Correct Answers: There are many valid ways to answer this question. The easiest answer is to decrease the gap score to a very low value. This causes an optimal alignment to be of length 2. Another easy answer is to choose γ > α . This causes an optimal alignment with only gaps. Incorrect Answers: It was incorrect to try to change the parameters to cause no mismatches. There are no mismatches in the optimal alignment. However, you were give partial credit based upon your reasoning. 2. Correct Answers: Two interpretations of the problem were given full credit. In one interpretation, you must have a proper suffix–prefix alignment. In this interpretation, you are not allowed to use the entirety of either string. The second correct interpretation allows the use of the entirety of a string (e.g. a prefix of A can be A itself). This second interpretation still requires using a suffix of A and a prefix of B . The difference between these two interpretations is mostly in the initialization of the table. For the interpretation requiring proper suffixes and prefixes, the first row of the table is initialized to −∞ , while for a interpretation allowing all of A to be used, we initialize the first row as we would for global alignment. In both cases, the first column is initialized with zeros....
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- Fall '06
- The Table, Correctness, γ, β