What is the best way to assemble a genome?
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
Which is better DNA plat forms?
Shorter reads cause of lower accurancy
Longer reads easier to assemble
Shorter reads cause of higher accurancy
Longer reads harded to assemble
What happens next after you have fragments?
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
How do you increase the coverage for genome sequencing?
Decrease the number of sequencing
Increase the number of sequencing
Use more DNA
Use reference DNA
Sequence gap:
Don't have enough sequence but know the order and orientation of the contigs
No information about the adjacent gap or spanning gap
Physical Gaps:
Know the order and orientation of the contigs but dont have enough sequence
What is the function of genome scaffolds?
Rearrange the genome
Rearrange gene
Construct and arrange contigs in relation to one another
Place contigs on a stiff sufface
What step is after contig production when you are trying to build a gemone?
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
Why would you no fill the gap that is found between contigs on the genome scaffold?
A customer might only want a scaffold of the genome
Gaps can be over looked
Customer might want to fill it in himself
What does N50 mean?
The value of which 50% of nucleotides sequences are represented
The percentage of gaps in the scaffold
The number of genes produced
A k-mer are nucleotides that have been cut down to a certain size
What is the function of a contig?
Represent a consensus region of DNA
Represent the genome
Represent the gene
Represent a consensus region of RNA
How can you guess gap sizes on scaffold?
Incorporating info from pair ends of the contigs
Randomly guess
Place all the contigs beneath each other
Long insert library
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
Why is De Novo genome assembly useful?
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
Why is the De Bruijn Graph useful?
Suitable for high coverage and long reads
Suitable for high coverage and short reads
How long do the k-mers need to be in overlap-layout-consensus?
approx 24
approx 2
approx 240
approx 2400
Why do the k mers in the De Bruijn model need to be similar sizes?
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
What is problem that arises when assembling fragments?
Repeats
mRNA
cDNA
gDNA
How do you solve the problem of repeats in genome assembly?
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
What takes up 45% of the genome?
Large duplications
Simple repeats
Introns and Exons
Transposons
Intergenic DNA have parasitic DNA that often fail to replicate properly
What is the name of the process whereby an exon from Gene A is placed in Gene B?
Exon duplication
Exon Shuffling
Intron Duplication
Intron Shuffling
What is the process whereby an exon is repeated and forms a new gene variant?
Exon Duplication
Entire gene families can be duplicated
What happens when entire gene super families get duplicated?
Can double the number of copies of every gene and gene family
Can half the number of copies of every gene and gene family
What happens when misaligned chromatids
Exons
Introns
Homologous genes in different organisms that encode proteins with the same function and have evolved by direct vertical descent
Orthologous Genes
Paralogous Genes
Homologous genes within an organism encoding proteins with related functions and often arise due to gene duplication
Orthologous genes
Paralogous genes
