Alexandra McCabe
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Third Year Gene's and Genomes Quiz on Peter Ritchie's Test, created by Alexandra McCabe on 26/05/2015.

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Alexandra McCabe
Created by Alexandra McCabe about 9 years ago
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Peter Ritchie's Test

Question 1 of 29

1

What is the best way to assemble a genome?

Select one or more of the following:

  • 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

Explanation

Question 2 of 29

1

Which is better DNA plat forms?

Select one or more of the following:

  • Shorter reads cause of lower accurancy

  • Longer reads easier to assemble

  • Shorter reads cause of higher accurancy

  • Longer reads harded to assemble

Explanation

Question 3 of 29

1

What happens next after you have fragments?

Select one or more of the following:

  • 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

Explanation

Question 4 of 29

1

How do you increase the coverage for genome sequencing?

Select one or more of the following:

  • Decrease the number of sequencing

  • Increase the number of sequencing

  • Use more DNA

  • Use reference DNA

Explanation

Question 5 of 29

1

Sequence gap:

Select one or more of the following:

  • Don't have enough sequence but know the order and orientation of the contigs

  • No information about the adjacent gap or spanning gap

Explanation

Question 6 of 29

1

Physical Gaps:

Select one or more of the following:

  • No information about the adjacent gap or spanning gap

  • Know the order and orientation of the contigs but dont have enough sequence

Explanation

Question 7 of 29

1

What is the function of genome scaffolds?

Select one or more of the following:

  • Rearrange the genome

  • Rearrange gene

  • Construct and arrange contigs in relation to one another

  • Place contigs on a stiff sufface

Explanation

Question 8 of 29

1

What step is after contig production when you are trying to build a gemone?

Select one or more of the following:

  • 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

Explanation

Question 9 of 29

1

Why would you no fill the gap that is found between contigs on the genome scaffold?

Select one or more of the following:

  • A customer might only want a scaffold of the genome

  • Gaps can be over looked

  • Customer might want to fill it in himself

Explanation

Question 10 of 29

1

What does N50 mean?

Select one or more of the following:

  • The value of which 50% of nucleotides sequences are represented

  • The percentage of gaps in the scaffold

  • The number of genes produced

Explanation

Question 11 of 29

1

A k-mer are nucleotides that have been cut down to a certain size

Select one of the following:

  • True
  • False

Explanation

Question 12 of 29

1

What is the function of a contig?

Select one or more of the following:

  • Represent a consensus region of DNA

  • Represent the genome

  • Represent the gene

  • Represent a consensus region of RNA

Explanation

Question 13 of 29

1

How can you guess gap sizes on scaffold?

Select one or more of the following:

  • Incorporating info from pair ends of the contigs

  • Randomly guess

  • Place all the contigs beneath each other

Explanation

Question 14 of 29

1

Long insert library

Select one or more of the following:

  • 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

Explanation

Question 15 of 29

1

Why is De Novo genome assembly useful?

Select one or more of the following:

  • 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

Explanation

Question 16 of 29

1

Why is the De Bruijn Graph useful?

Select one or more of the following:

  • 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

Explanation

Question 17 of 29

1

How long do the k-mers need to be in overlap-layout-consensus?

Select one or more of the following:

  • approx 24

  • approx 2

  • approx 240

  • approx 2400

Explanation

Question 18 of 29

1

Why do the k mers in the De Bruijn model need to be similar sizes?

Select one or more of the following:

  • 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

Explanation

Question 19 of 29

1

What is problem that arises when assembling fragments?

Select one or more of the following:

  • Repeats

  • mRNA

  • cDNA

  • gDNA

Explanation

Question 20 of 29

1

How do you solve the problem of repeats in genome assembly?

Select one or more of the following:

  • 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

Explanation

Question 21 of 29

1

What takes up 45% of the genome?

Select one or more of the following:

  • Large duplications

  • Simple repeats

  • Introns and Exons

  • Transposons

Explanation

Question 22 of 29

1

Intergenic DNA have parasitic DNA that often fail to replicate properly

Select one of the following:

  • True
  • False

Explanation

Question 23 of 29

1

What is the name of the process whereby an exon from Gene A is placed in Gene B?

Select one or more of the following:

  • Exon duplication

  • Exon Shuffling

  • Intron Duplication

  • Intron Shuffling

Explanation

Question 24 of 29

1

What is the process whereby an exon is repeated and forms a new gene variant?

Select one or more of the following:

  • Exon Duplication

  • Exon Shuffling

  • Intron Duplication

  • Intron Shuffling

Explanation

Question 25 of 29

1

Entire gene families can be duplicated

Select one of the following:

  • True
  • False

Explanation

Question 26 of 29

1

What happens when entire gene super families get duplicated?

Select one or more of the following:

  • Can double the number of copies of every gene and gene family

  • Can half the number of copies of every gene and gene family

Explanation

Question 27 of 29

1

What happens when misaligned chromatids

Select one or more of the following:

  • Repeats

  • Transposons

  • Exons

  • Introns

Explanation

Question 28 of 29

1

Homologous genes in different organisms that encode proteins with the same function and have evolved by direct vertical descent

Select one or more of the following:

  • Orthologous Genes

  • Paralogous Genes

Explanation

Question 29 of 29

1

Homologous genes within an organism encoding proteins with related functions and often arise due to gene duplication

Select one or more of the following:

  • Orthologous genes

  • Paralogous genes

Explanation

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