FAST3 and related tools MCQs With Answer

Introduction:

This blog provides a focused set of multiple-choice questions on FASTA3 and related sequence-search tools tailored for M.Pharm students. It covers core concepts such as the FASTA suite components, translation-frame searches, scoring matrices (PAM/BLOSUM), statistical measures (E-value, bit score), low-complexity masking, gap penalties, and practical choices between FASTA and BLAST. Questions emphasize interpretation of results and how these tools support pharmaceutical research tasks—target identification, homology detection, and conserved motif discovery for drug design and safety assessment. The MCQs are concise yet probing, ideal for exam preparation and applied understanding in computational biotechnology contexts.

Q1. What is the primary purpose of the FASTA/FASTA3 sequence-search suite?

• Identify regions of local similarity between sequences
• Construct global multiple sequence alignments of many sequences
• Predict tertiary protein structure from sequence
• Annotate metabolic pathways automatically

Correct Answer: Identify regions of local similarity between sequences

Q2. Which FASTA3 program implements a rigorous Smith–Waterman local alignment (exact dynamic programming)?

• FASTA
• SSEARCH
• BLAST
• CLUSTALW

Correct Answer: SSEARCH

Q3. Which FASTA program translates a nucleotide query into amino acids and searches a protein database?

• FASTX
• FASTY
• TFASTX
• SSEARCH

Correct Answer: FASTX

Q4. Which FASTA program compares a protein query against a nucleotide database translated in six frames?

• FASTX
• TFASTX
• SSEARCH
• BLASTP

Correct Answer: TFASTX

Q5. Which substitution matrix is commonly recommended for aligning very closely related protein sequences (short, high-identity matches)?

• PAM30
• BLOSUM62
• PAM250
• BLOSUM45

Correct Answer: PAM30

Q6. Which tool is used to mask low-complexity regions in protein sequences before similarity searches?

• SEG
• DUST
• CD-HIT
• TRF

Correct Answer: SEG

Q7. What does the E-value reported by FASTA/BLAST represent?

• Expected number of alignments with this score (or better) found by chance in the database search
• Exact percentage identity of the alignment
• Absolute alignment score without statistical normalization
• Number of gaps in the best alignment

Correct Answer: Expected number of alignments with this score (or better) found by chance in the database search

Q8. What is the bit score in sequence similarity searches?

• Raw alignment score dependent on substitution matrix and gap penalties
• Normalized alignment score independent of database size expressed in bits
• Number of matching residues in the alignment
• Length of the alignment multiplied by percent identity

Correct Answer: Normalized alignment score independent of database size expressed in bits

Q9. In alignment scoring, what is the gap opening penalty?

• Cost to initiate a gap in the alignment (gap opening penalty)
• Cost per residue for extending an existing gap
• Penalty for mismatched base pairs only in nucleotide alignments
• Penalty applied to low-complexity regions

Correct Answer: Cost to initiate a gap in the alignment (gap opening penalty)

Q10. Which method in FASTA uses a k-tuple (ktup) hashing heuristic to accelerate database searches?

• FASTA
• SSEARCH
• BLAST
• MUSCLE

Correct Answer: FASTA

Q11. Which FASTA variant is specifically designed to allow frameshift-aware comparison of a translated nucleotide query to protein sequences?

• FASTY
• FASTX
• SSEARCH
• BLASTX

Correct Answer: FASTY

Q12. When is BLAST generally preferred over the FASTA suite in routine database searching?

• When rapid searches of very large sequence databases are required (speed prioritized)
• When exact Smith–Waterman alignments are required for all hits
• When detecting very subtle, low-identity homologs with maximum sensitivity
• When performing de novo protein structure prediction

Correct Answer: When rapid searches of very large sequence databases are required (speed prioritized)

Q13. Which is a primary application of FASTA/BLAST searches in pharmaceutical research?

• Identify homologous proteins for target validation and conserved-residue analysis
• Directly predict clinical trial outcomes from sequence
• Measure drug solubility from sequence data alone
• Simulate enzyme kinetics without experimental data

Correct Answer: Identify homologous proteins for target validation and conserved-residue analysis

Q14. How many reading frames are considered when translating a nucleotide sequence for protein-database searches?

• Three
• Six
• One
• Nine

Correct Answer: Six

Q15. Which substitution matrix option is typically chosen to detect more distant protein homologs?

• PAM250
• PAM30
• BLOSUM80
• BLOSUM90

Correct Answer: PAM250

Q16. What does a lower E-value indicate about an alignment hit?

• Greater statistical significance of the match (less likely by chance)
• Lower alignment score and lower quality match
• Higher number of gaps in the alignment
• Shorter alignment length always

Correct Answer: Greater statistical significance of the match (less likely by chance)

Q17. Which algorithm underlies exact local alignment search implemented by SSEARCH?

• Needleman–Wunsch global alignment
• Smith–Waterman local alignment
• Neighbor-joining phylogeny
• Progressive multiple alignment

Correct Answer: Smith–Waterman local alignment

Q18. Which substitution matrix family is derived from observed substitutions in conserved blocks of protein families?

• BLOSUM
• PAM
• Identity matrix
• EDNAFULL

Correct Answer: BLOSUM

Q19. In translated-search contexts, what is a frameshift?

• An insertion or deletion that changes the reading frame during translation
• A substitution that changes one amino acid to another
• A masked low-complexity region
• A type of substitution matrix

Correct Answer: An insertion or deletion that changes the reading frame during translation

Q20. Which tool is commonly used to mask low-complexity regions in nucleotide sequences prior to database searching?

• DUST
• SEG
• TRF
• CD-HIT

Correct Answer: DUST

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