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cs-312:project-5 [2015/02/21 11:20]
ringger [Provided Framework]
cs-312:project-5 [2015/02/21 11:23]
ringger [Further Exploration]
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 Be sure that you are using the latest .NET framework: Bring up the properties of your project (can use the key-chord Alt+F7). For the property "​Target framework:",​ specify .NET Framework 4 (or higher). Be sure that you are using the latest .NET framework: Bring up the properties of your project (can use the key-chord Alt+F7). For the property "​Target framework:",​ specify .NET Framework 4 (or higher).
 +
 +Summary:
 +* For each pair of genes, you will apply the DP algorithm to compute their alignment cost.
 +* You will summarize the alignment costs for all pairs in the results table (the 10 x 10 table) in the GUI.  The results table is just a way of presenting the results. ​
  
 == Required: Whiteboard Experience (TM) == == Required: Whiteboard Experience (TM) ==
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 #Experiment with alternative operator (substitution,​ match, indel) costs and discuss the impact of changing their values. #Experiment with alternative operator (substitution,​ match, indel) costs and discuss the impact of changing their values.
 #Try aligning longer (sub-)sequences. ​ Conduct an empirical analysis. ​ Discuss impact on the alignment score matrix. #Try aligning longer (sub-)sequences. ​ Conduct an empirical analysis. ​ Discuss impact on the alignment score matrix.
-#​Re-implement your alignment algorithm in top-down fashion using recursion and a memory function. ​ How does this algorithm compare to the implementation ​using a table?+#​Re-implement your alignment algorithm in top-down fashion using recursion and a memory function. ​ How does this algorithm compare to the iterative, bottom-up ​implementation?​
 #Try a shortest-path algorithm like Dijkstra’s to solve this problem. #Try a shortest-path algorithm like Dijkstra’s to solve this problem.
 #Get ahead of the game, learn about the A* shortest-path algorithm, and implement it with a tight admissible heuristic (we will get to this topic later in the course, but you might enjoy trying it in the context of the alignment problem). #Get ahead of the game, learn about the A* shortest-path algorithm, and implement it with a tight admissible heuristic (we will get to this topic later in the course, but you might enjoy trying it in the context of the alignment problem).
cs-312/project-5.txt · Last modified: 2015/03/04 09:58 by ringger
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