Chapter 3 | DNA Sequensing
Multiple-Choice Questions:
1. What is the primary purpose of BLAST?
a) To find regions of similarity between biological sequences.
b) To predict protein structures.
c) To perform phylogenetic analysis.
d) To identify genetic mutations.
2. Which types of sequences can BLAST compare?
a) Nucleotide sequences only.
b) Protein sequences only.
c) Both nucleotide and protein sequences.
d) Neither nucleotide nor protein sequences.
3. What does the BLAST E-value represent?
a) The number of expected hits of similar quality that could be found just by
chance.
b) The statistical significance of the alignment score.
c) The length of the query sequence.
d) The size of the database being searched.
4. How can the E-value be used in a BLAST search?
a) As a measure of query sequence length.
b) To sort the search results by alignment score.
c) To filter the search results based on a desired threshold.
d) To estimate the number of expected hits in the database.
5. What is the formula for calculating the bit-score (S) in BLAST?
a) S = (λ × S − lnK)/ln2
b) S = E × ln2
c) S = λ + K
d) S = 2 × E
6. What does the bit-score indicate in BLAST?
a) The number of expected hits in the database.
b) The query coverage percentage.
c) The sequence similarity.
d) The size of the database.
7. What is the purpose of query coverage in BLAST?
a) To estimate the statistical significance of the alignment.
b) To determine the length of the target sequence.
c) To calculate the E-value.
d) To measure how much of the query sequence is covered by the alignment.
8. What is the format of BLAST "query" sequences?
a) FASTA format.
b) CSV format.
c) XML format.
d) Binary format.
BLAST Multiple Choice Questions (MCQ):
1. Which specialized search tool is used to find proteins highly similar to your
query?
a) SmartBLAST
b) Primer-BLAST
c) Global Align
d) CD-search
2. Which specialized search tool is used to design primers specific to your PCR
template?
a) SmartBLAST
b) Primer-BLAST
c) Global Align
d) CD-search
3. Which specialized search tool is used to compare two sequences across their
entire span using Needleman-Wunsch algorithm?
a) SmartBLAST
b) Primer-BLAST
c) Global Align
d) CD-search
4. Which specialized search tool is used to find conserved domains in your
sequence?
a) SmartBLAST
b) Primer-BLAST
c) Global Align
d) CD-search
5. Which specialized search tool is used to search immunoglobulins and T cell
receptor sequences?
a) SmartBLAST
b) Primer-BLAST
c) IgBLAST
d) CD-search
6. Which specialized search tool is used to search sequences for vector
contamination?
a) SmartBLAST
b) Primer-BLAST
c) VecScreen
d) CD-search
7. Which specialized search tool is used to find sequences with similar conserved
domain architecture?
a) SmartBLAST
b) Primer-BLAST
c) CDART
d) CD-search
8. Which specialized search tool is used to align sequences using domain and
protein constraints?
a) SmartBLAST
b) Primer-BLAST
c) Global Align
d) Multiple Alignment
9. Which specialized search tool is used to establish taxonomy for uncultured or
environmental sequences?
a) SmartBLAST
b) Primer-BLAST
c) MOLE-BLAST
d) CD-search
10. Which option allows you to download BLAST databases and executables?
a) SmartBLAST
b) Use BLAST API
c) Use BLAST in the cloud
d) Download BLAST
11. Which option allows you to call BLAST from your applications?
a) SmartBLAST
b) Use BLAST API
c) Use BLAST in the cloud
d) Download BLAST
12. Which option allows you to start an instance at a cloud provider to use
BLAST?
a) SmartBLAST
b) Use BLAST API
c) Use BLAST in the cloud
d) Download BLAST
True or False:
10. BLAST compares nucleotide or protein sequences to sequence databases and
calculates the statistical significance. True
11. The E-value represents the number of expected hits of similar quality that
could be found by chance and should high as possible as can. Fasle
12. The bit-score is dependent on the size of the database being searched. False
13. Query cover describes how much of the query sequence is covered by the
alignment. True
14. BLAST databases are constructed from concatenated FASTA-formatted
sequences. True
15. The formatdb program produces a mixture of binary- and ascii-encoded files
for BLAST databases. True
