Midterm (Version B) Solutions Fall 2024

PwnHero BME501/CPS501 Bioinformatics Midterm, Oct. 24, 2024 B SOLUTIONS Answer all questions on the question pages, right below the question. Time limit: 1 h 50 m No aids of any kind, including no calculators. You can express values as fractions if necessary. 1. Algorithm and Python (5 points): Write a function match_with_gap(seq1, seq2, gap_position) where seq1 and seq2 are DNA sequences with seq2 being one base longer than seq1, and gap_position is an integer from 0 to len(seq1), inclusive. The function returns True if a gap placed at gap_position in seq1 makes the letters of seq1 line up perfectly with those of seq2, and False otherwise. For example, match_with_gap(‘CATGAA’, ‘CATCGAA’, 3) would return True, since in the alignment: CAT-GAA (where the gap is at position 3) CATCGAA the letters of seq1 line up perfectly with the letters of seq2 (thanks to the gap). In this examle, if the 3 were any other value, the function would return False. def match_with_gap(seq1, seq2, gap_position) : # code here return seq1[0 : gap_position] == seq2[0 : gap_position] and seq1[gap_position:] == seq2[gap_position + 1 : ] This could be coded as a loop in place of slices in the following way: # first part for i in range(0, gap_position) : if seq1[i] != seq2[i] : return False # second part for i in range(gap_position, len(seq1)) : if seq1[i] != seq2[i+1] : return False # matched everwhere so .. return True PwnHero.com