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Peter Ritchie's Test

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Third Year Gene's and Genomes Quiz on Peter Ritchie's Test, created by Alexandra McCabe on 26/05/2015.
Alexandra McCabe
Quiz by Alexandra McCabe, updated more than 1 year ago
Alexandra McCabe
Created by Alexandra McCabe about 9 years ago
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Resource summary

Question 1

Question
What is the best way to assemble a genome?
Answer
  • Have a reference gene to different species
  • Have a reference gene to same species
  • Have a reference genome to same species
  • Have a reference genome to different species

Question 2

Question
Which is better DNA plat forms?
Answer
  • Shorter reads cause of lower accurancy
  • Longer reads easier to assemble
  • Shorter reads cause of higher accurancy
  • Longer reads harded to assemble

Question 3

Question
What happens next after you have fragments?
Answer
  • Place contigs together to see where they fit on the reference genome
  • Place contigs together next to eachother
  • Analyse each contig
  • Place contigs far apart

Question 4

Question
How do you increase the coverage for genome sequencing?
Answer
  • Decrease the number of sequencing
  • Increase the number of sequencing
  • Use more DNA
  • Use reference DNA

Question 5

Question
Sequence gap:
Answer
  • Don't have enough sequence but know the order and orientation of the contigs
  • No information about the adjacent gap or spanning gap

Question 6

Question
Physical Gaps:
Answer
  • No information about the adjacent gap or spanning gap
  • Know the order and orientation of the contigs but dont have enough sequence

Question 7

Question
What is the function of genome scaffolds?
Answer
  • Rearrange the genome
  • Rearrange gene
  • Construct and arrange contigs in relation to one another
  • Place contigs on a stiff sufface

Question 8

Question
What step is after contig production when you are trying to build a gemone?
Answer
  • Genome scaffolds with gaps in between contigs
  • Join contigs using evidence from pair end data
  • Place the contigs right next to eachother with no gaps

Question 9

Question
Why would you no fill the gap that is found between contigs on the genome scaffold?
Answer
  • A customer might only want a scaffold of the genome
  • Gaps can be over looked
  • Customer might want to fill it in himself

Question 10

Question
What does N50 mean?
Answer
  • The value of which 50% of nucleotides sequences are represented
  • The percentage of gaps in the scaffold
  • The number of genes produced

Question 11

Question
A k-mer are nucleotides that have been cut down to a certain size
Answer
  • True
  • False

Question 12

Question
What is the function of a contig?
Answer
  • Represent a consensus region of DNA
  • Represent the genome
  • Represent the gene
  • Represent a consensus region of RNA

Question 13

Question
How can you guess gap sizes on scaffold?
Answer
  • Incorporating info from pair ends of the contigs
  • Randomly guess
  • Place all the contigs beneath each other

Question 14

Question
Long insert library
Answer
  • 4-40 kb library that has 100 bp on each end
  • 4-8 kb library that has 100 bp on each end
  • 4-40 kb library that has 10 bp on each end
  • 4-8 kb library that has 10 bp on each end

Question 15

Question
Why is De Novo genome assembly useful?
Answer
  • Suitable for short coverage and long reads
  • Suitable for long coverage and long reads
  • Suitable for long coverage and short reads
  • Suitable for short coverage and short reads

Question 16

Question
Why is the De Bruijn Graph useful?
Answer
  • Suitable for high coverage and long reads
  • Suitable for high coverage and short reads
  • Suitable for short coverage and long reads
  • Suitable for short coverage and short reads

Question 17

Question
How long do the k-mers need to be in overlap-layout-consensus?
Answer
  • approx 24
  • approx 2
  • approx 240
  • approx 2400

Question 18

Question
Why do the k mers in the De Bruijn model need to be similar sizes?
Answer
  • If they are too small, it won't show overlaps
  • If they are too long, it won't show overlaps
  • If they are too small is easier to sequence
  • If they are too long is easier to sequence

Question 19

Question
What is problem that arises when assembling fragments?
Answer
  • Repeats
  • mRNA
  • cDNA
  • gDNA

Question 20

Question
How do you solve the problem of repeats in genome assembly?
Answer
  • Increase reading length which decreases sequence error rate
  • Increase reading length which increases sequence error rate
  • Decrease reading length which decreases sequence error rate
  • Decrease reading length which increases sequence error rate

Question 21

Question
What takes up 45% of the genome?
Answer
  • Large duplications
  • Simple repeats
  • Introns and Exons
  • Transposons

Question 22

Question
Intergenic DNA have parasitic DNA that often fail to replicate properly
Answer
  • True
  • False

Question 23

Question
What is the name of the process whereby an exon from Gene A is placed in Gene B?
Answer
  • Exon duplication
  • Exon Shuffling
  • Intron Duplication
  • Intron Shuffling

Question 24

Question
What is the process whereby an exon is repeated and forms a new gene variant?
Answer
  • Exon Duplication
  • Exon Shuffling
  • Intron Duplication
  • Intron Shuffling

Question 25

Question
Entire gene families can be duplicated
Answer
  • True
  • False

Question 26

Question
What happens when entire gene super families get duplicated?
Answer
  • Can double the number of copies of every gene and gene family
  • Can half the number of copies of every gene and gene family

Question 27

Question
What happens when misaligned chromatids
Answer
  • Repeats
  • Transposons
  • Exons
  • Introns

Question 28

Question
Homologous genes in different organisms that encode proteins with the same function and have evolved by direct vertical descent
Answer
  • Orthologous Genes
  • Paralogous Genes

Question 29

Question
Homologous genes within an organism encoding proteins with related functions and often arise due to gene duplication
Answer
  • Orthologous genes
  • Paralogous genes
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