Free Practice Quiz Question List

7 Computational Methods and Tools Online Quiz Questions

Use this free practice quiz with 20 questions to review 7 Computational Methods and Tools, test your knowledge, and prepare for your next test or exam.

20 questions

Choose one

1 point

Two long protein sequences differ substantially overall, but you want to find a short region they may share. Which method is the best fit for this goal?

A
Needleman–Wunsch global alignment
B
Smith–Waterman local alignment
C
Benjamini–Hochberg adjustment
D
K-mer indexing

True or false

1 point

A p-value is the probability, assuming the null hypothesis and statistical model are true, of observing a result at least as extreme as the one obtained.

A
True
B
False

Written response

1 point

A base has a Phred quality score of Q20. What is its estimated base-calling error probability, expressed as a percentage?

Fill in the blank

1 point

K-mer indexes support rapid read mapping by storing the of short sequence words.

Choose one

1 point

An analysis consists of several steps whose outputs become inputs to later steps. Which tool category is designed to express these steps and dependencies and help automate repeatable runs?

A
A substitution matrix
B
A statistical test
C
A workflow manager
D
A sequence identifier

Choose all

1 point

Select all accurate statements about the Benjamini–Hochberg false-discovery-rate method.

A
It adjusts interpretation across a set of tests.
B
It guarantees that every result called significant is correct.
C
It controls the expected proportion of false discoveries among results called significant under the method’s assumptions.
D
It is the probability that the null hypothesis is true for each result.

True or false

1 point

BLAST exhaustively calculates every possible alignment in a database before reporting its results.

A
True
B
False

Written response

1 point

A researcher wants to group similar biological samples. What computational method is used to form such groups?

Fill in the blank

1 point

For a workflow to be easier to reproduce, document or fix at least one of its .

Choose one

1 point

When aligning two protein sequences, a scoring scheme should distinguish among different amino-acid substitutions. Which tool is designed to provide those substitution scores?

A
A method that estimates the number of chance matches in a database search
B
A matrix that assigns scores to amino-acid substitutions
C
A workflow manager that orders dependent analysis steps
D
A quality scale that reports sequencing error probability

Choose all

1 point

Select all accurate statements about parallel computation in bioinformatics.

A
Dividing work across processors can reduce runtime.
B
It makes poor-quality input reliable by itself.
C
It can distribute independent work, such as processing separate samples.
D
It ensures that analysis parameters are appropriate.

Open ended

1 point

You need to test whether a set of sequencing reads supports a biological variant. Describe a basic analysis plan from defining the question through reporting the conclusion. Include how you would check the inputs, choose and document the method, assess the result, and make the analysis reproducible.

True or false

1 point

A reproducible workflow is automatically scientifically valid.

A
True
B
False

Choose one

1 point

An alignment method requires work proportional to the product of two sequence lengths, written as $m \times n$ . What is a practical implication when comparing very long sequences?

A
The work remains constant as both sequences grow.
B
The work depends only on the shorter sequence.
C
The work can become costly as the sequence lengths grow.
D
The method necessarily uses no memory.

Choose one

1 point

A read-mapping task repeatedly searches a large collection of sequences. Which strategy can speed up the search by organizing locations of short sequence words in advance?

A
Clustering sequences by a chosen similarity threshold
B
Indexing locations of short sequence words to support rapid read mapping
C
Dividing sample processing among multiple processors
D
Filling a dynamic-programming table to find an optimal alignment

Written response

1 point

You need to compare two sequences across their full lengths using a classic dynamic-programming alignment method. What is the name of the global alignment algorithm?

Choose one

1 point

Two proteins differ substantially overall, but you suspect they share a short conserved motif. Which approach best targets that question?

A
Use global alignment because it compares the complete sequences
B
Use clustering because it groups similar sequences
C
Use local alignment to find the strongest matching subsections
D
Use parallel computation because it divides work among processors

Choose one

1 point

You must search a large sequence database for candidate similarities and need a practical search rather than calculating every possible alignment. Which tool is the best fit?

A
Needleman–Wunsch, because it exhaustively calculates a global alignment
B
BLAST, because it uses a heuristic search to find promising matches efficiently
C
Smith–Waterman, because it exhaustively calculates local alignments
D
A workflow manager, because it selects the best alignment scoring scheme

Choose one

1 point

A sequencing dataset contains some low-quality bases, but aggressive trimming might remove genuine biological signal. What is the most appropriate preprocessing plan?

A
Remove all records that do not match the expected biological result
B
Trim every sequence by the same number of bases, regardless of quality
C
Apply preprocessing only when justified by documented criteria, while considering possible signal loss
D
Skip input checks because preprocessing will correct any file or metadata problems

Written response

1 point

A base has a Phred quality score of Q30. What estimated base-calling error probability does this represent? Give the value as a percentage.