MBT 540 Homework Assignment 4

Due Monday Feb. 11

1. Write a program that does the following, for the same genome sequence you used in assignments 1-3:
   1. Finds the 5 highest scoring non-overlapping segments of the sequence, for the scoring scheme that attaches +1 to an A or T nucleotide, and -2 to a G or C (assign 0 to any ambiguity characters in the sequence). Your program should first find the highest scoring segment, then scan the parts of the genome outside that segment to find the next highest-scoring segment, etc until you have found all 5.
   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 output should provide
   • the name and first line of the .fna file
   • for each of the scoring schemes, a list of the segments, giving the location where it occurs (the first and last nucleotide positions), and its score. Do NOT include the sequence of the segment, which may be very long.
2. Email this to me at phg@u.washington.edu. 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.