CSE 180 UPDATED 2026 EXAM SCRIPT QUESTIONS AND
ANSWERS GRADED A+
✔✔STOP and Think: Look again at the four most frequent 9-mers in the oriC region of
Vibrio cholerae. Now do you notice anything surprising and if so which strings are most
interesting
"ATGATCAAG", "CTTGATCAT", "TCTTGATCA", "CTCTTGATC" - ✔✔ATGATCAAG
and CTTGATCAT
✔✔Which strand is more prone to undergo deamination? - ✔✔Lagging
✔✔STOP and Think: Should we give up on determining which 9-mere is the most
important? If not, what would you do now? - ✔✔False
✔✔reverse half-strand is leading or lagging? - ✔✔Leading
✔✔Forward half-strand is leading or lagging? - ✔✔Lagging
✔✔STOP and Think: Is it safe to conclude that "ATGATCAAG"/"CTTGATCAT" also
represents a DnaA box in other bacterial genomes if it represents a DnaA box in one
bacteria - ✔✔False
✔✔Parent parent daughter daughter - ✔✔Conservative model
✔✔Parent daughter parent daughter - ✔✔Semi-conservative model
✔✔Part of parent part of daughter - ✔✔Dispersive model
✔✔Replication begins in a genomic region called the - ✔✔replication origin
✔✔some gene therapy methods use genetically engineered mini-genomes called -
✔✔Viral Vectors
✔✔Why are viral vectors called viral vectors? - ✔✔Because they are able to penetrate
cell walls
✔✔C is more frequent on the ___ half-strand - ✔✔Leading
✔✔G is less freqent on the ___ half-strand - ✔✔Leading
✔✔oriC is at Minimum or Maximum Skew? - ✔✔Minimum
, ✔✔Hidden messages tend to cluster 2.6.3 - ✔✔True
✔✔STOP and Think: Can you find the hidden message in
1
"atgaccgggatactgataaaaaaaagggggggggcgtacacattagataaacgtatgaagtacgttagactcggcgc
cgccg"
2
"acccctattttttgagcagatttagtgacctggaaaaaaaatttgagtacaaaacttttccgaataaaaaaaaaggggggg
a"
3
"tgagtatccctgggatgacttaaaaaaaagggggggtgctctcccgatttttgaatatgtaggatcattcgccagggtccga
"
4
"gctgagaattggatgaaaaaaaagggggggtccacgcaatcgcgaaccaacgcggacccaaaggcaagaccgat
aaaggaga"
5
"tcccttttgcggtaatgtgccgggaggctggttacgtagggaagccctaacggacttaataaaaaaaagggggggcttat
ag"
6
"gtcaatcatgttcttgtgaatggatttaaaaaaaaggggggggaccgcttggcgcacccaaattcagtgtgggcgagcgc
aa"
7
"cggttttggcccttgttagaggcccccgtaaaaaaaagggggggcaattatgagagagctaatctatcgcgtgcgtgttca
t"
8
"aacttgagttaaaaaaaagggggggctggggcacatacaagaggagtcttccttatcagttaatgctgtatgacactatgt
a"
9
"ttggcccattggctaaaagcccaacttgacaaatggaagatagaatccttgcataaaaaaaagggggggaccgaaag
ggaag"
10
"ctggtgagcaacgacagattcttacgtgcattagctcgcttccggggatctaatagcacgaagcttaaaaaaaaggggg
gg - ✔✔aaaaaaaaggggggggg
✔✔Do you see any potential issues with the proposed BruteForceMotifSearch
algorithm? - ✔✔Slow
✔✔STOP and Think: Why does GreedyMotifSearch perform so poorly? - ✔✔Zeroes
✔✔STOP and Think: How would you implement an algorithm for generating a random
integer? - ✔✔random.randint(1, M)
ANSWERS GRADED A+
✔✔STOP and Think: Look again at the four most frequent 9-mers in the oriC region of
Vibrio cholerae. Now do you notice anything surprising and if so which strings are most
interesting
"ATGATCAAG", "CTTGATCAT", "TCTTGATCA", "CTCTTGATC" - ✔✔ATGATCAAG
and CTTGATCAT
✔✔Which strand is more prone to undergo deamination? - ✔✔Lagging
✔✔STOP and Think: Should we give up on determining which 9-mere is the most
important? If not, what would you do now? - ✔✔False
✔✔reverse half-strand is leading or lagging? - ✔✔Leading
✔✔Forward half-strand is leading or lagging? - ✔✔Lagging
✔✔STOP and Think: Is it safe to conclude that "ATGATCAAG"/"CTTGATCAT" also
represents a DnaA box in other bacterial genomes if it represents a DnaA box in one
bacteria - ✔✔False
✔✔Parent parent daughter daughter - ✔✔Conservative model
✔✔Parent daughter parent daughter - ✔✔Semi-conservative model
✔✔Part of parent part of daughter - ✔✔Dispersive model
✔✔Replication begins in a genomic region called the - ✔✔replication origin
✔✔some gene therapy methods use genetically engineered mini-genomes called -
✔✔Viral Vectors
✔✔Why are viral vectors called viral vectors? - ✔✔Because they are able to penetrate
cell walls
✔✔C is more frequent on the ___ half-strand - ✔✔Leading
✔✔G is less freqent on the ___ half-strand - ✔✔Leading
✔✔oriC is at Minimum or Maximum Skew? - ✔✔Minimum
, ✔✔Hidden messages tend to cluster 2.6.3 - ✔✔True
✔✔STOP and Think: Can you find the hidden message in
1
"atgaccgggatactgataaaaaaaagggggggggcgtacacattagataaacgtatgaagtacgttagactcggcgc
cgccg"
2
"acccctattttttgagcagatttagtgacctggaaaaaaaatttgagtacaaaacttttccgaataaaaaaaaaggggggg
a"
3
"tgagtatccctgggatgacttaaaaaaaagggggggtgctctcccgatttttgaatatgtaggatcattcgccagggtccga
"
4
"gctgagaattggatgaaaaaaaagggggggtccacgcaatcgcgaaccaacgcggacccaaaggcaagaccgat
aaaggaga"
5
"tcccttttgcggtaatgtgccgggaggctggttacgtagggaagccctaacggacttaataaaaaaaagggggggcttat
ag"
6
"gtcaatcatgttcttgtgaatggatttaaaaaaaaggggggggaccgcttggcgcacccaaattcagtgtgggcgagcgc
aa"
7
"cggttttggcccttgttagaggcccccgtaaaaaaaagggggggcaattatgagagagctaatctatcgcgtgcgtgttca
t"
8
"aacttgagttaaaaaaaagggggggctggggcacatacaagaggagtcttccttatcagttaatgctgtatgacactatgt
a"
9
"ttggcccattggctaaaagcccaacttgacaaatggaagatagaatccttgcataaaaaaaagggggggaccgaaag
ggaag"
10
"ctggtgagcaacgacagattcttacgtgcattagctcgcttccggggatctaatagcacgaagcttaaaaaaaaggggg
gg - ✔✔aaaaaaaaggggggggg
✔✔Do you see any potential issues with the proposed BruteForceMotifSearch
algorithm? - ✔✔Slow
✔✔STOP and Think: Why does GreedyMotifSearch perform so poorly? - ✔✔Zeroes
✔✔STOP and Think: How would you implement an algorithm for generating a random
integer? - ✔✔random.randint(1, M)
