7/12/23, 10:36 PM Module 3 | Coursera

Module 3
Back Due Jul 30, 11:59 PM CEST
Graded Quiz • 30 min • 10 total points

Module 3: Edit distance, assembly,

overlaps

Quiz

Quiz: Module 3
Module 3
1. The value in each edit-distance matrix element depends on its neighbors: 1 point

Quiz • 30 min
10 questions To the left and to the lower-left
Programming Homework To the upper-left, to the left and to the lower-left

Above, to the left, and to the upper-left

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Above, to the left, and to the right
Due Jul 30, 11:59 PM CEST Attempts 3 every 8 hours

2. Say we have filledReceive

in the approximate
grade matching matrix and identified the minimum value (say, 2) in the bottom 1 point
Your grade
row. Now we would like to know the shape of the corresponding 2-edit alignment, i.e. we would like to know View Feedback
To Pass 70%
where the insertions, or higher
deletions and substitutions are. We use a procedure called: 50% We keep your highest score

Filling

Pathing
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Binary search

Traceback

3. Say the edit distance between DNA strings α and β is 407. What is the edit distance between α and βG (β 1 point
concatenated with the base G)?

could be any of the other choices

406

407

408

4. Say we are using dynamic programming to find approximate occurrences of P in T. About how many dynamic 1 point
programming matrix elements do we have to fill in?

|T|^2 (squared)

|P|^2 (squared)

|P| + |T|

|P| |T|

5. Local alignment is different from global alignment because: 1 point

Insertions and deletions incur no penalty

There is no dynamic programming algorithm for solving it

It compares three strings instead of two

It finds similarities between substrings rather than between entire strings

6. The first law of assembly says that if a prefix of read A is similar to a suffix of read B, then... 1 point

A and B should not be joined in the final assembly

A and B must be from different genomes

Read B might have a sequencing error at the end

A and B might overlap in the genome

7. The second law of assembly says that more coverage leads to... 1 point

more and longer overlaps between reads

more sequencing errors

less accurate results

8. In an overlap graph, the nodes of the graph correspond to 1 point

Bases

Reads

Genomes

Overlaps

9. The overlap graph is a useful structure because: 1 point

It makes it faster to compare reads

It helps to ignore long overlaps

A reconstruction of the genome corresponds to a path through the graph

10. Which of the following is not a reason why an overlap might contain sequence differences (i.e. might not be an 1 point
exact match):

Sequencing error

Insufficient coverage

Polyploidy

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