Problem Set #1, Genome 559

Due Tues, January 17, 2017, at the beginning of class. Assignments turned in more than 10 minutes after the beginning of class will be penalized.
NOTE - your programs should work with other command-line arguments, not just the ones provided as examples.

1. (10 points) You can find a copy of the BLOSUM62 protein substitution matrix at ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62. Which amino acid has the smallest variance in scores associated with it? Why? Which has the largest variance? Why? (do your best, your answer can be biochemical or evolutionary and requires knowledge outside of this course)
   

2. (15 points)

   RLINLMP----KVLAREYKNY
   QFFPLMPPAPYKILAKDFENY

   Score the above protein alignment using

   • BLOSUM62 and a linear gap penalty of -4
   • BLOSUM40 with affine gap penalties: gap open of -9 and gap extension of -1.

   You can find the BLOSUM80 protein substitution matrix at ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM40. Be sure to show your work.

3. (20 points) Draw and fill in the dynamic programming matrix to align these two sequences: TGCTG and TAATG. Use this substitution matrix:

   	A	C	G	T
   A	2	-4	-2	-6
   C	-4	2	-6	-2
   G	-2	-6	2	-6
   T	-6	-2	-6	2

   and use a fixed gap penalty of -5. What is the score of the optimal global alignment?

4. (10 points) Write a program that takes as input the first three command line arguments (after the program name) and prints them in uppercase with each argument on a separate line. For example:
   

   > python get-three-args1.py con stan tinople
   CON 
   STAN 
   TINOPLE

5. (15 points) Write a program similar to the previous one, but print the three arguments on one line without spaces between them.

   > python get-three-args2.py con stan tinople
   CONSTANTINOPLE

6. (15 points) Write a program that takes as input three command line arguments: the first argument is a DNA or protein sequence (or any string really), and the second and third represent a range of positions in the sequence. Print the range of characters in the given sequence.

   > python get-subsequence.py cantankerous 5 7
   ank

7. (15 points) Write a program that takes as input two command line arguments, counts how many times the first one appears inside the second one, and then tells the user how many there are.

   > python count-substrings.py acg acgtacgtttgacgtacc
   The sequence acg appears in the sequence acgtacgtttgacgtacc 3 times.

8. Challenge questions (no points but I do look at them if you include an answer) Write a program that takes as input a single string and makes as output the reverse of the string. Write a program that takes as input a DNA sequence and makes as output its reverse complement. Do the same thing except retain the case of characters in the input sequence (case is often used to indicate things like exons vs introns). Do the same thing but impose a requirement that the input characters be valid nucleotides ('A', 'C', 'G', or 'T' or their lowercase equivalents) - provide a useful error message if not.
   

   > python reverse.py acgtac
   catgca
   
   > python reverse-complement1.py acgtac
   gtacgt
   
   > python reverse-complement2.py acGTac
   gtACgt
   
   > python reverse-complement3.py acGTac
   gtACgt
   
   > python reverse-complement3.py acJTac
   Input error: character J not a valid nucleotide