quiz 1

Question 1

cutie

Answer 1

pie

Question 2

What is bioinformatics?

Answer 2

Bioinformatics concerns the generation, visualization, analysis, storage, and retrieval of large quantities of biological information.

Question 3

How has bioinformatics impacted biomedical research?

Answer 3

Bioinformatics has revolutionized biomedical research.

Question 4

What must be done to raw biomedical data to derive meaningful information?

Answer 4

Raw data must be analyzed, annotated, reformatted, mostly automated using bioinformatics software, and graphically represented.

Question 5

Define DNA sequencing.

Answer 5

DNA sequencing is the process of determining the order of nucleotide bases in a DNA molecule.

Question 6

What is Sanger sequencing?

Answer 6

Sanger sequencing produces .ab1 files that can be analyzed by Chromas or Geneious.

Question 7

Name three platforms used in next-generation sequencing (NGS).

Answer 7

• Illumina
• Ion Torrent
• PacBio

Question 8

What type of file is produced by Oxford Nanopore sequencing?

Answer 8

The file produced is fast5.

Question 9

What are assembly files in genomics?

Answer 9

Assembly files include contigs and scaffolds, stored in FASTA format, and annotation files that provide information on gene locations and functions.

Question 10

What is genome mapping?

Answer 10

Genome mapping is the process of determining the physical location of genes and other genomic features on a chromosome.

Question 11

What is structural genomics?

Answer 11

Structural genomics is the study of the three-dimensional structure of proteins and macromolecules encoded by an organism’s genome.

Question 12

What techniques are used in structural genomics?

Answer 12

• X-ray crystallography
• NMR spectroscopy
• Electron microscopy

Question 13

Define functional genomics.

Answer 13

Functional genomics is the study of the functional properties of genes and genomic elements.

Question 14

What are some methods used in functional genomics?

Answer 14

• Gene expression profiling
• RNA interference
• Genome editing

Question 15

What is comparative genomics?

Answer 15

Comparative genomics is the study of similarities and differences between the genomes of different organisms.

Question 16

Name two prominent examples of genomic data projects.

Answer 16

• The 1000 Genomes Project
• The Cancer Genome Atlas (TCGA)

Question 17

What is the approximate size of the human genome?

Answer 17

The human genome is approximately 3.2 billion nucleotides long.

Question 18

What is GenBank?

Answer 18

GenBank is a huge repository run by the US National Center for Biotechnology Information (NCBI).

Question 19

What is sequence alignment?

Answer 19

Sequence alignment is a method to compare two or more nucleotide or protein sequences to identify similarities and differences.

Question 20

What is the difference between global and local alignment?

Answer 20

• Global alignment: compares highly similar sequences
• Local alignment: compares sequences of different lengths with high variability

Question 21

What is genome assembly?

Answer 21

Genome assembly is the process of piecing together fragments of DNA sequences to reconstruct the complete genome of an organism.

Question 22

What are the two types of genome assembly?

Answer 22

• De novo assembly
• Reference-based assembly

Question 23

Define phylogenetics.

Answer 23

Phylogenetics is the study of the evolutionary relationships between organisms based on their genetic and morphological characteristics.

Question 24

What is gene annotation?

Answer 24

Gene annotation is the process of identifying details such as gene locations, similarities, and associations with phenotypes.

Question 25

What is functional annotation?

Answer 25

Functional annotation is the process of identifying the functions of genes or proteins by analyzing their sequence and interaction networks.

Question 26

What are some applications of bioinformatics in drug discovery?

Answer 26

* Screening of chemical libraries * Computer-aided drug design * Drug development studies

Question 27

What is personalized medicine?

Answer 27

Personalized medicine is an approach to treatment that considers individual differences in genetics, environment, and lifestyle.

Question 28

What are some challenges in bioinformatics?

Answer 28

* Data storage and management * Data integration and analysis * Ethics and privacy

Question 29

What is the role of machine learning in bioinformatics?

Answer 29

Machine learning can accelerate the analysis of large biological data sets but requires careful validation.

Question 30

What is the purpose of the NCBI?

Answer 30

The NCBI provides access to a wide range of biological databases and resources.

Question 31

What is UniProt?

Answer 31

UniProt is a comprehensive database of protein sequences and functional information.

Question 32

What does KEGG stand for?

Answer 32

Kyoto Encyclopedia of Genes and Genomes.

Question 33

What is Expasy?

Answer 33

Expasy is a resource offering bioinformatics tools and databases related to protein analysis.

Question 34

What does NCBI stand for?

Answer 34

National Center for Biotechnology Information ## Footnote NCBI provides access to various biological databases.

Question 35

What is the purpose of the NCBI's Entrez?

Answer 35

It serves as an interface between users and data, facilitating searches across multiple databases. ## Footnote Entrez is the search engine used by NCBI.

Question 36

List three resources that can be accessed through NCBI.

Answer 36

* GenBank * PubMed * UniProt

Question 37

What type of information does the UniProt database provide?

Answer 37

Protein sequence and functional information. ## Footnote UniProt is a collaboration among EMBL-EBI, SIB, and PIR.

Question 38

What does PubMed cover?

Answer 38

A very large literature database covering all major journals of biology and medicine.

Question 39

What are Medical Subject Headings (MeSH) used for in PubMed?

Answer 39

They are used to index queries for searching literature.

Question 40

Fill in the blank: Gene names can often be considered a _______.

Answer 40

moving target

Question 41

What is the official gene symbol for 'kibra'?

Answer 41

WWC1

Question 42

What is OMIM?

Answer 42

Online Mendelian Inheritance in Man

Question 43

What types of records does OMIM contain?

Answer 43

* Human genes * Human disorders thought to be genetic * Associated phenotypes

Question 44

How can you limit your search to only nucleotide sequences in NCBI?

Answer 44

Change the menu from 'All Databases' to 'Nucleotide'.

Question 45

What is Gene Ontology?

Answer 45

An approach to answer questions related to protein functions, locations, and associations.

Question 46

What does the Gene Database at NCBI compile?

Answer 46

Information from numerous sources on a single gene.

Question 47

What does the 'Genomic context' section display?

Answer 47

Adjacent genes portrayed as arrows on the chromosome.

Question 48

What is the function of the 'Genomic regions, transcripts, and products' section?

Answer 48

It shows a map of exons of transcripts along with accession numbers.

Question 49

True or False: The same laboratory can have multiple names for the same gene.

Answer 49

True

Question 50

What is the significance of the symbols next to the OMIM record numbers?

Answer 50

* (+) Associated phenotype * (#) Diseases where the gene defect is known * (%) Mapped disorders where the gene is still unknown * (*) For genes not associated with a phenotype

Question 51

What website can be used to search published information on a gene using synonyms?

Answer 51

iHOP (information Hyperlinked Over Proteins)

Question 52

What types of evidence can be found in Gene Ontology?

Answer 52

Various forms of data supporting or refuting scientific conclusions.

Question 53

What can be customized in PubMed searches?

Answer 53

* Filter display options * Hyperlinks * Advanced search * Exporting files