Bioinformatics and Genomics

Question 1

Which bases are purine and which are pyrimidine?

Answer 1

Purine: A, G
Pyrimidine: C, T (& U)

Question 2

Is it 5’ to 3’, or 3’ to 5’?

Answer 2

5’ to 3’

Question 3

Which base in the codon is known as degenerate? (i.e. tends to be different but still code for the same aa)

Answer 3

The third base

Question 4

What is a locus?

Answer 4

A unique chromosomal location defining the position of a gene?

Question 5

What is an allele?

Answer 5

Alternative versions of a gene

Question 6

Define genotype

Answer 6

All alleles at a locus

Question 7

Which is shorter - the p or the q arm of a chromosome?

Answer 7

The p arm is shorter.

Question 8

When was sequencing the human genome (3 billion base pairs) completed?

Answer 8

2003

Question 9

How many protein coding genes?

Answer 9

Just over 20,000

Question 10

How many gene transcripts are known?

Answer 10

Over 200,000

Question 11

How many pairs of chromosomes do humans have?

Answer 11

23 pairs of chromosomes

Question 12

How many pairs of autosomes do humans have?

Answer 12

22 pairs of autosomes

Question 13

How much DNA is identical between 2 humans?

Answer 13

99. 9% is identical

0. 1% accounts for variation

Question 14

Threshold to describe a rare variant?

Answer 14

< 1% of the population

Question 15

Define a SNP

Answer 15

In genetics, a single-nucleotide polymorphism is a SUBSTITUTION of a single nucleotide at a specific position in the genome, that is present in a sufficiently LARGE FRACTION of the population (e.g. 1% or more)

Question 16

How long is a short/long read?

Answer 16

short read; <200-400 bp

long read; 10,000-100,000 bases

Question 17

What do depth and coverage refer to in sequence assembly/alignment?

Answer 17

Depth of coverage is the number of reads of a given nucleotide in an experiment.

Depth ~ how many times an individual base has been sequenced

Coverage ~ average time each base across an entire region has been sequenced. the average number of reads that align to, or “cover,” known reference bases.

Question 18

Example of a sequencer that produces long reads?

Answer 18

Oxford nanopore
(calculates resistance through pore)

Pac Bio

Question 19

Advantages of nanopore sequencing technology?

Answer 19

Small devices - portable, can be used in the field

Long reads, can handle trickier parts of genome

Question 20

When was the genomics england campaign launched?

Answer 20

2013

Question 21

What is pharamcogenomics?

Answer 21

The study of how genes affect a person’s response to drugs.