a few other issues regarding HW5 that popped up in the forum:
Q1 section A - the name of the function should be frequency. the exercise says ferquency which is a typo.
Q2 section C - you are not obligated to use a matrix for the storage of intermediate results. other data structures might do the job just as well. however, when solving this question, you are not allowed to make any recursive calls. remember the guidelines of DP: start by computing small values of N and then work your way up, store intermediate results in an elegant fashion.
Q4 - note that when opening the proteome files using notepad, the line break characters might "disappear", so the file would appear to have a single, very long line of text. this is since windows expects line breaks to contain 2 characters '\r\n' instead of just '\n'. if you open the same file in python, line breaks will appear normally. a forum post by itzikh explains this issue with great detail and historic background.