Tools for sequence analysis MCQs With Answer

Introduction: This quiz set on Tools for Sequence Analysis is designed specifically for M.Pharm students preparing for exams and practical applications in bioinformatics and computational biotechnology. It covers commonly used software and databases for sequence similarity searches, multiple sequence alignment, motif and domain detection, genome browsing, phylogenetics, and sequence-based predictions relevant to drug discovery and molecular pharmacology. Questions emphasize both conceptual understanding and tool-specific functions, helping students recognize appropriate workflows for target identification, variant analysis, primer design, and protein feature prediction. Use these MCQs to test knowledge, identify gaps, and reinforce practical choices when analyzing nucleotide and protein sequences in pharmaceutical research.

Q1. Which tool is primarily used for rapid local sequence similarity searches against large sequence databases?

• Primer3 for primer design
• BLAST for local sequence similarity searches
• MAFFT for multiple sequence alignment
• SignalP for signal peptide prediction

Correct Answer: BLAST for local sequence similarity searches

Q2. What is the main difference between BLASTn and BLASTp?

• BLASTn compares protein sequences; BLASTp compares nucleotide sequences
• BLASTn compares nucleotide sequences; BLASTp compares protein sequences
• BLASTn is used for multiple alignment; BLASTp is for phylogenetics
• BLASTn is a web browser; BLASTp is a database

Correct Answer: BLASTn compares nucleotide sequences; BLASTp compares protein sequences

Q3. Which multiple sequence alignment tool is optimized for very large numbers of sequences and scalability?

• Clustal Omega, optimized for large-scale alignments
• MUSCLE, only for pairwise alignments
• T-Coffee, designed exclusively for small datasets
• EMBOSS Water, primarily for genome browsing

Correct Answer: Clustal Omega, optimized for large-scale alignments

Q4. HMMER is best described as a tool for which of the following?

• Designing PCR primers using thermodynamic models
• Profile hidden Markov model-based searches for homology
• Visualizing genomic tracks in a browser
• Assembling short sequencing reads de novo

Correct Answer: Profile hidden Markov model-based searches for homology

Q5. Which tool is known for ultrafast short-read alignment to reference genomes, suitable for NGS reads?

• BWA and Bowtie are the same; choose any
• Bowtie, an ultrafast short-read aligner
• ORFfinder, for mapping short reads
• Pfam, for short-read alignment

Correct Answer: Bowtie, an ultrafast short-read aligner

Q6. Which program is widely used for manipulating alignment files (SAM/BAM) and performing basic variant calling?

• MEGA for SAM/BAM processing
• SAMtools for SAM/BAM manipulation and basic variant calling
• Jalview for read mapping
• SignalP for variant calling

Correct Answer: SAMtools for SAM/BAM manipulation and basic variant calling

Q7. Which tool is specialized for predicting classical signal peptides at the N-terminus of proteins?

• TMHMM for mitochondrial targeting sequences
• InterProScan for transmembrane helices only
• SignalP for signal peptide prediction
• Pfam for signal peptide cleavage site prediction

Correct Answer: SignalP for signal peptide prediction

Q8. For predicting transmembrane helices in membrane proteins, which tool is commonly used?

• BLAST for transmembrane helix prediction
• TMHMM for transmembrane helix prediction
• Primer3 for helix prediction
• MAFFT for membrane topology mapping

Correct Answer: TMHMM for transmembrane helix prediction

Q9. What is Pfam best described as?

• A short-read aligner database
• A protein family database based on profile HMMs
• A primer design toolkit
• A genome browser for human SNPs

Correct Answer: A protein family database based on profile HMMs

Q10. What primary function does InterProScan provide to researchers analyzing protein sequences?

• Combines multiple signature databases to annotate protein domains and functions
• Performs de novo genome assembly
• Designs CRISPR guide RNAs exclusively
• Converts protein sequences into nucleotide sequences

Correct Answer: Combines multiple signature databases to annotate protein domains and functions

Q11. Which tool is widely used for designing PCR primers and assessing primer properties?

• ORFfinder for primer melting temperature calculation
• Primer3 for PCR primer design
• EMBOSS Needle for primer design
• HMMER for primer specificity

Correct Answer: Primer3 for PCR primer design

Q12. ORFfinder is primarily used to do which of the following tasks?

• Predict transmembrane domains
• Identify open reading frames (ORFs) in nucleotide sequences
• Perform phylogenetic tree inference
• Search for motifs using HMMs

Correct Answer: Identify open reading frames (ORFs) in nucleotide sequences

Q13. The UCSC Genome Browser is most useful for which activity?

• Running local BLAST searches offline
• Visualizing genomic annotations and integrating multiple data tracks
• Designing multiple sequence alignments for proteins
• Predicting signal peptides in proteins

Correct Answer: Visualizing genomic annotations and integrating multiple data tracks

Q14. In which scenario is BLAT preferred over BLAST?

• When searching very distant homologs across kingdoms
• When requiring extremely sensitive remote-homology detection
• When aligning highly similar sequences quickly, such as mRNA to genome
• When performing de novo assembly of short reads

Correct Answer: When aligning highly similar sequences quickly, such as mRNA to genome

Q15. Which software package is commonly used by pharmacology students to build and visualize phylogenetic trees from aligned sequences?

• SignalP for phylogenetic tree building
• MEGA for phylogenetic analysis and tree visualization
• Bowtie for tree inference
• Pfam for tree visualization

Correct Answer: MEGA for phylogenetic analysis and tree visualization

Q16. Which tool is popular for visualizing and editing multiple sequence alignments with rich annotation features?

• Jalview for alignment visualization and editing
• BLAST for alignment editing
• ORFfinder as an alignment editor
• Bowtie for annotation of alignments

Correct Answer: Jalview for alignment visualization and editing

Q17. What is the EMBOSS suite best known for?

• A collection of sequence analysis tools for tasks like translation, motif searches, and format conversion
• A database of protein families based on HMMs
• A web-based genome browser only for bacterial genomes
• A de novo assembler for long reads

Correct Answer: A collection of sequence analysis tools for tasks like translation, motif searches, and format conversion

Q18. Within the HMMER suite, which program is appropriate to scan a protein sequence against a database of HMMs such as Pfam?

• hmmsearch, which queries HMMs against sequence databases
• hmmbuild, which scans sequences against HMM libraries
• hmmscan, which scans a protein sequence against an HMM database like Pfam
• phmmer, which builds HMMs from multiple alignments

Correct Answer: hmmscan, which scans a protein sequence against an HMM database like Pfam

Q19. Which multiple alignment file format is commonly required by many phylogenetic programs such as RAxML and PhyML?

• FASTQ format used for raw reads
• PHYLIP format often required by phylogenetic tools
• GFF3 format for alignments
• PNG image format for trees

Correct Answer: PHYLIP format often required by phylogenetic tools

Q20. Which suite is widely used for discovering statistically significant conserved motifs in DNA or protein sequences?

• MEME Suite for motif discovery
• Bowtie for motif discovery
• Clustal Omega for motif scoring only
• UCSC Genome Browser for de novo motif finding

Correct Answer: MEME Suite for motif discovery

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