Genomics

Question 1

Explain how a single sequence is turned into a genome (the steps)

Answer 1

1) Split the genome into manageable chunks
2) Work out which order they are in
3) Get the DNA sequence of each chunk
4) Put them together

Question 2

Describe what ‘shotgun’ sequencing is

Answer 2

1) Fragment genomic DNA
2) Clone into sequencing vector
3) Pick colonies and sequence

Question 3

Describe the steps of ‘shotgun’ sequencing for high throughput (next generation

Answer 3

1) Fragment genomic DNA , select sizes
2) Ligate adaptor oligos
3) Hybridise to complementary oligos on sequencing plate
4) Amplify
5) Sequence

Question 4

What is the HTS cycle?

Answer 4

1) Template (amplifies on the sequencing plate) added to growing chain 5’-3’
2) Detect label with a camera
3) Chemically cleave the label revealing the 3’ OH

Question 5

What is meant by the term contig?

Answer 5

A ‘contiguous’ (continous) consensus sequence from an assembly

Question 6

What is mean by the term scaffold?

Answer 6

A series of contigs where we have additional information to place them together in the right order and orientation but the sequence between the contigs is not complete

Question 7

What is meant by the term assembly?

Answer 7

The set of scaffolds for one genome

Question 8

What is meant by the term N50?

Answer 8

The size of the largest contig/scaffold of which 50% of the assembled data is in a contig/scaffold of that size or larger

Question 9

Describe protein coding genes

Answer 9

Generally not repetitive but there are some exceptions e,g fillagrin and high copy number genes

Question 10

What are the repetitive regions?

Answer 10

Microsatellites
Telomeres
Intron sequences

Question 11

What are transposons?

Answer 11

Mobile genetic elements- sequences of a few kb that can move about the genome. Thousands of copies in eukaryotes

Question 12

Describe what the read length is

Answer 12

-A single read cannot span a repetitive region that is longer that the read length. This prevents long contigs from forming. The longer the read length, the larger the repeat region that can be assembled

Question 13

Describe read depth/coverage

Answer 13

-The average number of times each base appears is the final assembly. A coverage of 10x means that each base is on average found in 10 reads. The deeper the coverage, the more clearly any sequence or structure changes can be discerned from sequence error

Question 14

Describe what ploidy is

Answer 14

The number of copies of the genome in the organism