Biological Databases and Data Retrieval: Master the Fundamentals

Question 1

Which database is widely known for its vast repository of nucleotide sequences?

Accepted Answer

GenBank

Answer

Protein Data Bank (PDB)

Answer

UniProt

Question 2

Which of the following is NOT a recognized primary biological database?

Accepted Answer

Google Scholar

Answer

GenBank

Answer

PDB

Answer

PubMed

Question 3

What is the primary data format utilized by GenBank for representing nucleotide sequences?

Accepted Answer

FASTA

Answer

PDB

Answer

XML

Answer

JSON

Question 4

Which search strategy is most appropriate when aiming to identify protein sequences sharing similarity to a known sequence?

Accepted Answer

Sequence similarity search

Answer

Keyword search

Answer

Structure similarity search

Answer

Functional annotation search

Question 5

What distinguishes the Protein Data Bank (PDB) as a valuable resource in bioinformatics?

Accepted Answer

It provides access to experimentally determined 3D structures of proteins

Answer

It allows users to conduct molecular simulations

Answer

It contains comprehensive information on protein sequences

Answer

It offers specialized tools for protein visualization

Question 6

Which file format is predominantly used for storing and representing protein structures in databases?

Accepted Answer

PDB

Answer

FASTA

Answer

XML

Answer

CSV

Question 7

What is a key advantage of using well-curated biological databases in scientific research?

Accepted Answer

They provide quick access to trustworthy and high-quality biological data

Answer

They make data collection and analysis unnecessary

Answer

They contain all available biological data

Answer

They ensure data is free of errors and biases

Question 8

Which of the following is the primary nucleotide sequence database maintained by the National Center for Biotechnology Information (NCBI)?

Accepted Answer

GenBank

Answer

RefSeq

Answer

Protein Data Bank

Answer

PubMed

Question 9

Which search method in BLAST exhibits the highest sensitivity to variations within nucleotide sequences?

Accepted Answer

TBLASTN

Answer

BLASTN

Answer

BLASTP

Answer

BLASTX

Question 10

PubMed is a database that primarily contains:

Accepted Answer

Scientific literature related to biomedicine

Answer

Complete genome sequences

Answer

Protein structures

Answer

Gene expression data

Question 11

Which tool is commonly used for visualizing and analyzing protein structures?

Accepted Answer

PyMOL

Answer

ClustalW

Answer

NCBI BLAST

Answer

PubMed

Question 12

The Protein Data Bank (PDB) database primarily contains information about:

Accepted Answer

Protein structures

Answer

Protein sequences

Answer

Nucleotide sequences

Answer

Gene expression profiles

Question 13

Which biological database primarily stores DNA sequence data?

Accepted Answer

GenBank

Answer

Protein Data Bank (PDB)

Answer

PubChem

Answer

PubMed

Question 14

What is the data format commonly employed to store protein structure information?

Accepted Answer

PDB

Answer

FASTA

Answer

XML

Answer

JSON

Question 15

For retrieving sequences similar to a specific gene, which search strategy is most appropriate?

Accepted Answer

Basic Local Alignment Search Tool (BLAST)

Answer

Hidden Markov Model (HMMER)

Answer

ClustalW

Answer

Phylogenetic tree construction

Question 16

To visualize protein structures, which of the following tools is commonly used?

Accepted Answer

PyMOL

Answer

Microsoft Excel

Answer

Adobe Photoshop

Answer

Notepad

Question 17

In GenBank, what data field serves as a unique identifier for each sequence?

Accepted Answer

Accession number

Answer

Organism name

Answer

Sequence length

Answer

Publication date

Question 18

Which database houses information pertaining to gene expression data?

Accepted Answer

Gene Expression Omnibus (GEO)

Answer

European Nucleotide Archive (ENA)

Answer

Sequence Read Archive (SRA)

Answer

Protein Data Bank (PDB)

Question 19

What is the primary output format for sequence alignment results obtained using BLAST?

Accepted Answer

FASTA

Answer

XML

Answer

PDB

Answer

Comma-separated values (CSV)

Question 20

Which database is curated and maintained by the European Bioinformatics Institute (EBI)?

Accepted Answer

UniProt

Answer

PubMed

Answer

GenBank

Answer

Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)

Question 21

Which file format is exclusively used to represent protein structure information in the Protein Data Bank (PDB)?

Accepted Answer

.pdb

Answer

.csv

Answer

.fasta

Answer

.xml

Question 22

Which database serves as the primary repository for DNA sequences?

Accepted Answer

GenBank

Answer

PubMed

Answer

UniProt

Answer

EMBL-EBI

Question 23

What is the full name of the BLAST algorithm?

Accepted Answer

Basic Local Alignment Search Tool

Answer

Biomarker Local Alignment Search Technology

Answer

Biological Large-scale Alignment Search Technique

Answer

Bioinformatics Local Alignment Search Tool

Question 24

What is the primary purpose of the FASTA format in bioinformatics?

Accepted Answer

Representing nucleotide or protein sequences in a text-based format

Answer

Storing protein structure data

Answer

Visualizing biological pathways

Question 25

Which of the following databases is dedicated to providing information on gene expression data?

Accepted Answer

Gene Expression Omnibus (GEO)

Answer

UniProt

Answer

Protein Data Bank (PDB)

Answer

GenBank

Question 26

Define a protein domain.

Accepted Answer

A conserved segment of amino acids that performs a specific function

Answer

A non-functional region of a protein

Answer

A complete protein molecule

Question 27

Which software tool is commonly used for visualizing protein structures in 3D?

Accepted Answer

PyMOL

Answer

Notepad

Answer

Microsoft Word

Answer

Excel

Question 28

Explain the fundamental difference between a nucleotide and a nucleoside.

Accepted Answer

A nucleoside lacks a phosphate group, while a nucleotide possesses one.

Answer

A nucleotide contains a double helix structure

Answer

There is no difference between a nucleotide and a nucleoside

Answer

A nucleotide lacks a sugar group

Question 29

Which database is primarily utilized for identifying protein-protein interactions?

Accepted Answer

STRING

Answer

PDB

Answer

GenBank

Answer

UniProt