Structural Genomics

Question 1

What are the two types of databases for genome projects

Answer 1

• General: GenBank and GenomeBrowser
• Specific: Influenza Research Database, PopFly and FlyBase

Question 2

As ______ advances, so does the development of ______ which results in the ____________

Answer 2

• Computer connectivity
• Molecular technologies
• Establishment of public sequence databases

Question 3

What is a biological database?

Answer 3

• A large body of data organized to give access to information
  Allows for:
• connectivity between databases
• tools for servers and analyses
• training and tutorials to understand how to do things

Question 4

what is a GenBank accession number

Answer 4

A unique identifier for a sequence record. It has a combination of letters and numbers that indicate types of molecules

Question 5

What kind of information can be found on a genome sequence

Answer 5

• Open Reading Frames (ORFs) and proteins
• Regions of interest like promoter regions and receptor binding regions
• Protein domains

Question 6

What is a RT-PCR Primer

Answer 6

• A number of primer sets from around the world used to find viruses in biological samples

Question 7

What is structural genomics

Answer 7

An assembly of contiguous stretched of chromosomal DNA

Question 8

List the three types of genomics

Answer 8

• Structural genomics
• Functional genomics; characterizing the role played by transcripts and proteins
• Comparative genomics; comparing he genomes of different organisms

Question 9

How are whole genomes generated?

Answer 9

By;
- Sequencing and assembly
- A desired level of quality—for variable
- Annotation for function

Question 10

What is the Hierarchical Genome Shotgun (HGS) approach to sequencing the human genome

Answer 10

• Using random markers to fragment genome and the map of the fragments are organized
• The minimum amount of overlapping clones are sequenced repeatedly and the adjacent clones are merged

Question 11

What is the Whole Genome Shotgun (WGS) approach to sequencing the human genome

Answer 11

• The whole genome is fragmented into pieced then, sequenced.
• A series of overlapping DNA sequences are used to build the map
• The pieces are assembled into contigs that span across each chromosome
• It is faster and cheaper than HGS, but when two genome regions are similar in sequence, they’re lumped together creating gaps

Question 12

What is the difference between WGS and HGS?

Answer 12

• In WGS, the entire genome is cut randomly into small fragments without being mapped and then reassembled. In HGS, the genome is first mapped with clones chosen and then sequenced.

Question 13

What is the problem during the assembly of sequence date from the WGS method?

Answer 13

There is no map to tell the true order of the sequence so repetitive DNA and duplications can fit into different places
If putting he wrong place it can cause gaps in the sequence

Question 14

How is the problem pertaining to the WGS method solved?

Answer 14

If the end reads of two different contigs are recognized within a vector, the paired-ends will indicate they belong together physiologically and no gaps are created.

Question 15

How are genomes mapped?

Answer 15

we can look at variations of DNA based on the coinheritance of molecular markers

Question 16

What techniques are used you obtain fingerprints?

Answer 16

• RFLP: Restriction Fragment Length Polymorphism
• STS: Sequence-Tagged Sites

Question 17

Explain RFLP

Answer 17

• The fingerprint being obtain is cloned twice with overlapping sections
• These clones are placed on a band and read, the shared bands between the two indicates DNA sequence

Question 18

Explain STS

Answer 18

• This is used to amplify DNA sequences with PCR
• This will produce a simple and reproducible pattern on a gel
• The marker finds a site on the genome with PCR

Question 19

What is de novo sequencing

Answer 19

Determining the complete genome sequence of the first genome of a species but, you need to assemble it first because the genome is not present at first

Question 20

Describe resequencing

Answer 20

there is a reference genome from another species used to sequence the genome of interest
This genome is then mapped to the reference genome

Question 21

What is the recommended approach to sequencing

Answer 21

• The hybrid approach
• Whne you use WGS to produce a six fold coverage and map it
• A mini tiling path of duplicated DNA is produced for sequencing

Question 22

What are some indicators of genome completeness and quality?

Answer 22

• Per-base coverage (the average number of times a base is sequenced in a genome project
• N50 (the shortest contig lenght that needs to be included to cover 50% of the total assembly length

Question 23

What is coverage

Answer 23

• The number of sequence reads multiplied but the length of reads
• This is then divided by the genome size. This can be used to estimate the coverage
• A higher coverage is always desired

Question 24

explain the concept of N50

Answer 24

• A small N50 indicated the genome is fragmented and a large N50 indicates the genome has longer contigs
• There are 4 contigs of different lengths (5Kb, 4Kb, 2Kb and 1Kb) with a sum of 12Kb
• The N50 for this assembly will be 4 because the sum of the longest and second longest (5+4) divided by the sum of all lengths (12) is 75% which is greater than 50% (6)

Question 25

How is genome sequence data displayed?

Answer 25

• Graphics: showing the structure of the genome with details like exons and introns)
• GenBank: entries with descriptors
• FASTA: A universal file format used to report sequences followed by an actual sequence

Question 26

what is genome annotation