Bioinformatics

Question 1

What is transciptomics?

Answer 1

study of gene expression data

Question 2

What is GenBank?

Answer 2

Large datasets of DNA sequence

Question 3

What is in vivo?

Answer 3

traditional biological experiments within an organism

Question 4

What is in vitro?

Answer 4

traditional biological experiments in an artificial environment

Question 5

What is in silico?

Answer 5

On the computer

Question 6

What is bioinformatics?

Answer 6

Application of computer science for the management and analysis of biological information

Question 7

What are computers used for in bioinformatics?

Answer 7

GATHER biological data
STORE intelligently and efficiently
Provide TOOLS to allow extraction of meaningful biological information
MERGE information from several sources to increase understanding

Question 8

What is a primary database?

Answer 8

information about e.g. DNA sequences

Question 9

What is a secondary database?

Answer 9

contain results of analysis of primary resources e.g. sequence patterns or mutations

Question 10

What are the three main nucleotide sequence databases?

Answer 10

GenBank (National Center for Biotechnology Information -NCBI)
EBI -EMBL (European Molecular Biology Laboratory)
DDBJ (DNA Data Bank of Japan)

Question 11

What is easier to obtain protein or DNA sequences?

Answer 11

Protein sequences

Question 12

What is UniProtKB

Answer 12

(Universal Protein Resource Knowledgebase) – Comprehensive catalogue of information about proteins.

Question 13

What was the first protein to have its structure determined?

Answer 13

myoglobin

Question 14

What is Protein Data Bank (RCSB PDB)?

Answer 14

a protein data bank that stores over 100,000 structures

Question 15

How is bioinformatics used to annotate genomes?

Answer 15

identify genes, protein coding regions

predict structures and functions

Question 16

True or False?

Bioinformatics is a new research tool which will replace the need for laboratory experiments in the future

Answer 16

False

Experiments will still be needed as proof

Question 17

True or False?

A bioinformatics database is an archive or store of biological data

Answer 17

True

Question 18

True or False?

This is a nucleotide sequence ACTRFCGTRECATCGNKL

Answer 18

False

Protein sequence

Question 19

True or False?

Protein structures are more difficult to determine than protein sequences

Answer 19

True

Question 20

What is BLAST?

Answer 20

commonly used bioinformatics tool for rapidly comparing new sequences with known sequences e.g. All known nucleotide sequences

Question 21

What can you find out if you have the complete sequence of a gene?

Answer 21

Gene name, organism, complete gene + protein sequences

Information about protein’s function, structure, evolution

Question 22

Even if you don’t have the complete sequence of the gene you can still find out stuff about it.
What can you find out and how?

Answer 22

function, evolution etc from looking at related sequences
Because similar sequences may
have similar structure and/or function
have evolved from common ancestor

Question 23

What can use to find out more about the human genome?

Answer 23

http://www.genecards.org/

Question 24

What is http://www.ensembl.org/ ?

Answer 24

A whole genome browser
“software system which produces and maintains automatic annotation on selected eukaryotic genomes”
Can browse genome at different levels: chromosome ->gene->exon->nucleotide

Question 25

What is sequence alignment?

Answer 25

‘line up’ sequences so that similar features are in same columns

Question 26

What are ClustalW2 and Clustal omega

Answer 26

Most commonly used multiple sequence alignment program Can align DNA or protein sequences Requires fixed format input e.g. file with sequences in FASTA format

Question 27

What is shotgun sequencing?

Answer 27

copy DNA many times chop each up into many random fragments sequence each little piece (“read”) assemble fragments where they overlap

Question 28

What is functional annotation?

Answer 28

Finding out what genes are for by looking at what the proteins do

Question 29

Why would you rather use bioinformatics over experimental approaches to research functional annotation of genes?

Answer 29

Bioinformatics is a scaled up automatic approach making it much faster

Question 30

During functional annotations what should you find out about the proteins?

Answer 30

Are there related proteins? (BLAST search) – cautiously infer function from these Search secondary databases (e.g. SMART) for functional domains Predict 3D structure – help to determine function where sequences are only weakly related to known proteins

Question 31

What can you use genome sequencing for from a single genome?

Answer 31

What is necessary for life? Genes that control economically important traits e.g. crops Personalised medicine

Question 32

What can use genome sequencing for comparatively?

Answer 32

How have species evolved? | What makes humans unique? Only 1% of our genes have not been found in other species!