Nucleic acid databases MCQs With Answer

Nucleic Acid Databases MCQs With Answer

This quiz collection is designed specifically for M.Pharm students studying Bioinformatics and Computational Biotechnology. It focuses on nucleic acid databases, covering primary archival repositories (GenBank, EMBL-ENA, DDBJ), curated reference sets (RefSeq), specialized resources for non-coding RNAs, variant and population frequency databases (dbSNP, gnomAD), and expression/SRA archives. Questions also explore genome browsers, annotation conventions, submission types (WGS, TSA), and practical search tools (BLAST, BLAT). Each MCQ aims to deepen conceptual understanding and practical use of databases encountered in pharmacogenomics, target discovery, and translational research. Answers are provided for rapid self-assessment and exam preparation.

Q1. Which set of databases collectively forms the International Nucleotide Sequence Database Collaboration (INSDC)?

• GenBank, RefSeq, and Ensembl
• GenBank, EMBL-ENA, and DDBJ
• EMBL-ENA, UniProt, and PDB
• RefSeq, DDBJ, and UCSC

Correct Answer: GenBank, EMBL-ENA, and DDBJ

Q2. Which NCBI resource provides curated, non-redundant reference sequences for genomes, transcripts and proteins?

• GenBank
• RefSeq
• UniProtKB
• ENA

Correct Answer: RefSeq

Q3. In a FASTA file, which character begins the header line that describes the sequence?

• @
• >
• #
• ;

Correct Answer: >

Q4. When performing a nucleotide sequence similarity search using NCBI BLAST, which database should you select for a comprehensive nucleotide collection?

• nr
• nt
• swissprot
• pdb

Correct Answer: nt

Q5. Which archival repository is specifically intended for raw high-throughput sequencing reads?

• GEO
• SRA (Sequence Read Archive)
• ArrayExpress
• RefSeq

Correct Answer: SRA (Sequence Read Archive)

Q6. Which database is the primary NCBI repository for processed gene expression and array data?

• ArrayExpress
• GEO (Gene Expression Omnibus)
• SRA
• BioSample

Correct Answer: GEO (Gene Expression Omnibus)

Q7. What is the principal content of dbSNP?

• Protein structures and ligand interactions
• Single nucleotide polymorphisms and small insertions/deletions
• Non-coding RNA families
• Gene expression microarray designs

Correct Answer: Single nucleotide polymorphisms and small insertions/deletions

Q8. Which database models RNA families using covariance models and curated multiple alignments (often searched with Infernal)?

• miRBase
• RNAcentral
• Rfam
• SILVA

Correct Answer: Rfam

Q9. Which resource is the authoritative repository for microRNA sequences and annotation?

• Rfam
• miRBase
• NONCODE
• RefSeq

Correct Answer: miRBase

Q10. What is the purpose of RNAcentral?

• To host raw sequencing reads for RNA-Seq
• To aggregate non-coding RNA sequences from multiple expert databases into a unified resource
• To provide curated protein sequences
• To store clinical variant interpretations

Correct Answer: To aggregate non-coding RNA sequences from multiple expert databases into a unified resource

Q11. Which statement correctly describes a major difference between GenBank and RefSeq?

• GenBank is curated and non-redundant, RefSeq is archival and redundant
• RefSeq provides curated, non-redundant reference records while GenBank is an archival, submitter-provided collection that may be redundant
• GenBank contains only protein sequences, RefSeq contains only nucleotide sequences
• RefSeq is part of EMBL-ENA and GenBank is part of DDBJ

Correct Answer: RefSeq provides curated, non-redundant reference records while GenBank is an archival, submitter-provided collection that may be redundant

Q12. In the NCBI data model, what is the main difference between a BioProject and a BioSample?

• BioProject describes a biological specimen; BioSample groups related sequencing libraries
• BioProject groups related data from a research project; BioSample describes the individual biological material used for experiments
• BioSample is a publication record; BioProject is a raw read file
• They are synonymous and interchangeable

Correct Answer: BioProject groups related data from a research project; BioSample describes the individual biological material used for experiments

Q13. Which genomic resource provides the Variant Effect Predictor (VEP) and extensive gene/transcript annotation for many species?

• UCSC Genome Browser
• Ensembl
• GenBank
• Protein Data Bank (PDB)

Correct Answer: Ensembl

Q14. For archiving large-scale structural variation data (e.g., CNVs, large insertions/deletions), which NCBI database is most appropriate?

• dbSNP
• dbVar
• ClinVar
• RefSeq

Correct Answer: dbVar

Q15. Which population database is commonly used to retrieve allele frequency information for variant interpretation in clinical and pharmacogenomic studies?

• dbSNP
• gnomAD
• RefSeq
• Rfam

Correct Answer: gnomAD

Q16. In GenBank feature tables, which feature key is used to annotate a protein-coding region?

• gene
• CDS
• rRNA
• misc_feature

Correct Answer: CDS

Q17. In sequence submission categories, what does TSA stand for in GenBank/ENA nomenclature?

• Targeted Sequence Assembly
• Transcriptome Shotgun Assembly
• Total Sequence Archive
• Taxonomic Sequence Annotation

Correct Answer: Transcriptome Shotgun Assembly

Q18. Which alignment tool is optimized for very fast alignment of mRNA or long DNA sequences to a reference genome, particularly for large genomes like human?

• BLAST
• BLAT
• ClustalW
• MAFFT

Correct Answer: BLAT

Q19. For obtaining experimental three-dimensional structures of nucleic acids and nucleic-acid-containing complexes, which database should you query?

• PDB (Protein Data Bank)
• GenBank
• RefSeq
• RNAcentral

Correct Answer: PDB (Protein Data Bank)

Q20. Which controlled vocabulary is widely used for consistent annotation of sequence features (e.g., exon, CDS, intron) across genome databases?

• Gene Ontology (GO)
• Sequence Ontology (SO)
• Medical Subject Headings (MeSH)
• Protein Ontology (PRO)

Correct Answer: Sequence Ontology (SO)

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