homework1_sol

homework1_sol - Homework problems for CMSC423. Set 1 1...

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Unformatted text preview: Homework problems for CMSC423. Set 1 1 Global, local alignment matrices It is easy to modify the demo provided on the class page ( http://www.cs.umd. edu/class/fall2011/cmsc423/demos/align.html ) to allow different scores for pairs of letters. The matrix for global alignment will look like this: s 35 29 25 19 13 9 8 8 8 . . . . . . s 30 24 20 14 8 6 9 7 8 . . . . . . e 25 19 15 9 5 7 8 7 10 . . . . . . n 20 14 10 4 8 6 6 11 16 . . . . . e 15 9 5 6 4 7 12 17 22 . . . . . n 10 4 4 3 8 13 18 23 28 . . . . o 5 2 4 9 14 19 24 29 34 . . 5 10 15 20 25 30 35 40 n o n s e n s e You find the optimal alignment by looking at the right top corner and following the tracebacks all the way to the left bottom corner from where we started. 1 The matrix for local alignment will look like this: s- 1- 1 . . . ....
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homework1_sol - Homework problems for CMSC423. Set 1 1...

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