Do as much of this as you can; don't rush. Don't get frustrated - ask me or your neighbor for help. Hand in brief answers on Friday.
  1. Scoring effects: Use an online Needleman-Wunsch implementation (such as this one) to align the sequences "ctaatcattag" and "ctatatcttagg" with matches given +1, mismatches -2, and gaps -4. Why does this give a poor alignment? What is the best scoring system and corresponding alignment that you can find (it is sufficient to just vary the gap penalty)?

  2. Sequence similarity through dot plots: Use JDotter with a small window size (5 bases) to examine the nucleotide sequence found here. Compare your results to that of a random DNA sequence

  3. Intro to Python: From the Terminal program, type 
     python
    at the command prompt. Enter your first name as a string called MyName by typing 
     MyName = "Marshall"
    (with your name instead). We can "slice" this string of letters by using the array index notation MyName[start:stop:increment]. For example, try typing the following: 
    MyName[0:2]
    MyName[0:]
    MyName[1:2]
    MyName[::-1]
    Finally, as an exercise in "list comprehension", type 
    for letter in MyName: print letter