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cs-312:project-5 [2015/02/21 11:21]
ringger [Provided Framework]
cs-312:project-5 [2015/03/04 09:58]
ringger
Line 95: Line 95:
 # Align the first 100 characters (bases) of sequence #3 (row 3) and #10 (column 10) (assuming the first sequence in the table is numbered as #1); extract and display the alignment in your report using a fixed-width font.  For example, if you were aligning "​AGCTCATGCT"​ and "​ACTGCATCA",​ the side-by-side alignment should be presented in the manner shown here: # Align the first 100 characters (bases) of sequence #3 (row 3) and #10 (column 10) (assuming the first sequence in the table is numbered as #1); extract and display the alignment in your report using a fixed-width font.  For example, if you were aligning "​AGCTCATGCT"​ and "​ACTGCATCA",​ the side-by-side alignment should be presented in the manner shown here:
 <pre> <pre>
-AGCT-CATGCT +AGCTCATGCT 
-A-CTGCAT-CA+ACTGCAT-CA
 </​pre>​ </​pre>​
  
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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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