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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