Genome 540 Homework Assignment 4

Due Sunday Feb. 8

  1. Write a program to find a highest-weight path in a weighted directed acyclic graph. This program should
  2. Write a program that
  3. For the same genome sequence you used in HW assignments 1-3:
    1. Run the program in #2 above, using as input files the .fna file for that genome and a scoring scheme file that attaches +1 to an A or T nucleotide, and -2 to a G or C (and assigns 0 to any ambiguity characters in the sequence). Then run your program in #1 above on the resulting output file in order to find the highest scoring segment (= path) of the sequence. Use the first output option (i.e. printing path score, and where the path begins and ends, but not the complete list of edges).
    2. Same as above, but using the scoring scheme that attaches +1 to a G or C, and -2 to an A or T.
    Your final output should include
  4. Email the (final) output from #3 to me AND to Chris. Please make it as compact as possible. Do NOT send the code itself. Include the output in the body of your email message (as plain text), NOT as an attachment.