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cs-312:project-5 [2015/02/21 11:21] ringger [Provided Framework] |
cs-312:project-5 [2015/02/21 11:23] ringger [Further Exploration] |
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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). |