Bioinformatics Flashcards

1
Q

What is transciptomics?

A

study of gene expression data

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2
Q

What is GenBank?

A

Large datasets of DNA sequence

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3
Q

What is in vivo?

A

traditional biological experiments within an organism

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4
Q

What is in vitro?

A

traditional biological experiments in an artificial environment

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5
Q

What is in silico?

A

On the computer

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6
Q

What is bioinformatics?

A

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

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7
Q

What are computers used for in bioinformatics?

A

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

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8
Q

What is a primary database?

A

information about e.g. DNA sequences

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9
Q

What is a secondary database?

A

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

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10
Q

What are the three main nucleotide sequence databases?

A

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

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11
Q

What is easier to obtain protein or DNA sequences?

A

Protein sequences

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12
Q

What is UniProtKB

A

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

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13
Q

What was the first protein to have its structure determined?

A

myoglobin

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14
Q

What is Protein Data Bank (RCSB PDB)?

A

a protein data bank that stores over 100,000 structures

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15
Q

How is bioinformatics used to annotate genomes?

A

identify genes, protein coding regions

predict structures and functions

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16
Q

True or False?

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

A

False

Experiments will still be needed as proof

17
Q

True or False?

A bioinformatics database is an archive or store of biological data

18
Q

True or False?

This is a nucleotide sequence ACTRFCGTRECATCGNKL

A

False

Protein sequence

19
Q

True or False?

Protein structures are more difficult to determine than protein sequences

20
Q

What is BLAST?

A

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

21
Q

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

A

Gene name, organism, complete gene + protein sequences

Information about protein’s function, structure, evolution

22
Q

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?

A

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

23
Q

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

A

http://www.genecards.org/

24
Q

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

A

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

25
What is sequence alignment?
‘line up’ sequences so that similar features are in same columns
26
What are ClustalW2 and Clustal omega
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
27
What is shotgun sequencing?
copy DNA many times chop each up into many random fragments sequence each little piece (“read”) assemble fragments where they overlap
28
What is functional annotation?
Finding out what genes are for by looking at what the proteins do
29
Why would you rather use bioinformatics over experimental approaches to research functional annotation of genes?
Bioinformatics is a scaled up automatic approach making it much faster
30
During functional annotations what should you find out about the proteins?
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
31
What can you use genome sequencing for from a single genome?
What is necessary for life? Genes that control economically important traits e.g. crops Personalised medicine
32
What can use genome sequencing for comparatively?
How have species evolved? | What makes humans unique? Only 1% of our genes have not been found in other species!