# Finding Hidden Messages in DNA (Bioinformatics I) Quiz Answers

## All Weeks Finding Hidden Messages in DNA (Bioinformatics I)

### Finding Hidden Messages in DNA (Bioinformatics I) Week 01 Quiz Answers

Q1. True or False: The Finding oriC Problem is a well-defined computational problem.

• True
• False

Q2. Compute Count(ACTGTACGATGATGTGTGTCAAAG, TGT).

Q3. What is the most frequent 3-mer of CGCCTAAATAGCCTCGCGGAGCCTTATGTCATACTCGTCCT?

Q4. What is the reverse complement of TTGTGTC?

Q5. Solve the Pattern Matching Problem with Text = ATGACTTCGCTGTTACGCGC and Pattern = CGC to find all starting positions of Pattern in Text. Return the starting positions in increasing order (make sure to use 0-based indexing!)

E​nter your answer as a collection of space-separated integers. (e.g., 4 7 14)

### Finding Hidden Messages in DNA (Bioinformatics I) Week 02 Quiz Answers

Q1. True or False: Deamination is more likely to occur when DNA is single-stranded than when it is double-stranded.

• True
• False

Q2. Compute the Hamming distance between CTACAGCAATACGATCATATGCGGATCCGCAGTGGCCGGTAGACACACGT and

CTACCCCGCTGCTCAATGACCGGGACTAAAGAGGCGAAGATTATGGTGTG.

Q3. Identify the value of i for which Skew(CATTCCAGTACTTCGATGATGGCGTGAAGA) attains a minimum value.

Q4. Compute Count2(CATGCCATTCGCATTGTCCCAGTGA, CCC).

Q5. The d-neighborhood of the k-mer Pattern is the collection of all k-mers that are at most Hamming distance d from Pattern.

How many 10-mers are in the 1-neighborhood of Pattern = CCAGTCAATG?

Note that the d-neighborhood of Pattern includes Pattern.

### Finding Hidden Messages in DNA (Bioinformatics I) Week 03 Quiz Answers

Q1. Which type of algorithm selects the most attractive choice at each step?

• Dynamic programming algorithm
• Greedy algorithm
• Randomized algorithm
• Brute force search
• Combinatorial algorithm
• Machine learning algorithm

Q2. True or false: a motif of lowest score with respect to a collection of strings does not need to appear as a substring of one of the strings.

• True
• False

Q3. Order the following probability distributions from lowest to highest entropy:

A: (0.5, 0, 0, 0.5)

B: (0.25, 0.25, 0.25, 0.25)

C: (0, 0, 0, 1)

D: (0.25, 0, 0.5, 0.25)

• C, A, D, B
• D, C, A, B
• B, C, A, D
• B, A, D, C
• C, A, B, D

Q4. Consider the following profile matrix:

• A: 0.4 0.3 0.0 0.1 0.0 0.9
• C: 0.2 0.3 0.0 0.4 0.0 0.1
• G: 0.1 0.3 1.0 0.1 0.5 0.0
• T: 0.3 0.1 0.0 0.4 0.5 0.0

Q4. Which of the following strings is a consensus string for this profile matrix? (Select all that apply.)

• TCGCGA
• ACGCGA
• ACGTTA
• AGGTCA
• AAGCTA
• AAGAGA

Q5. Consider the following motif matrix:

CTCGATGAGTAGGAAAGTAGTTTCACTGGGCGAACCACCCCGGCGCTAATCCTAGTGCCC

GCAATCCTACCCGAGGCCACATATCAGTAGGAACTAGAACCACCACGGGTGGCTAGTTTC

GGTGTTGAACCACGGGGTTAGTTTCATCTATTGTAGGAATCGGCTTCAAATCCTACACAG

Which of the following 7-mers is a median string for this motif matrix? (Select all that apply.)

• AACGCTG
• ATAACGG
• GAACCAC
• GGTTACT
• AATCCTA
• CGTGTAA

Q6. Consider the following profile matrix Profile:

• A: 0.4 0.3 0.0 0.1 0.0 0.9
• C: 0.2 0.3 0.0 0.4 0.0 0.1
• G: 0.1 0.3 1.0 0.1 0.5 0.0
• T: 0.3 0.1 0.0 0.4 0.5 0.0

#### Finding Hidden Messages in DNA (Bioinformatics I) Week 04 Quiz Answers

Q1. True or False: RandomizedMotifSearch performs well when given a uniform profile matrix.

• True
• False

Q2. True or False: RandomizedMotifSearch and GibbsSampler are usually run on many choices of initial k-mers.

• True
• False

Q3. True or False: it is possible for GibbsSampler to move from a collection of motifs with lower score to a collection of motifs with higher score.

• True
• False

Q4. Which of the following motif-finding algorithms is guaranteed to find an optimum solution? In other words, which of the following are not heuristics? (Select all that apply.)

• RandomizedMotifSearch
• GreedyMotifSearch (without pseudocounts)
• GreedyMotifSearch (with pseudocounts)
• MedianString

Q5. Assume we are given the following strings Dna:

TGACGTTC

TAAGAGTT

GGACGAAA

CTGTTCGC

Then, assume that RandomizedMotifSearch begins by randomly choosing the following 3-mers Motifs of Dna:

• TGA
• GTT
• GAA
• TGT

What are the 3-mers after one iteration of RandomizedMotifSearch? In other words, what are the 3-mers Motifs(Profile(Motifs), Dna)? Please enter your answer as four space-separated strings.

#### Get All Course Quiz Answers of

Finding Hidden Messages in DNA (Bioinformatics I) Quiz Answers

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