Genomic Sequencing Advances Quiz
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Genomic Sequencing Advances Quiz

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@ReliableMookaite1890

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Questions and Answers

What is the purpose of a barcode in Illumina sequencing?

  • Enables simultaneous sequencing of multiple samples (correct)
  • Aids in forming clusters on the flow cell
  • Acts as a molecular tag for tracking individual DNA fragments
  • Helps in identifying the base interpreted from the color of a cluster

    • What is the function of adapters in Illumina workflow?

  • Known primers added to ends of DNA fragments (correct)
  • Contain short DNA sequences for tracking individual fragments
  • Enable simultaneous sequencing of multiple samples
  • Form clusters on the flow cell

    • What does a flow cell in Illumina sequencing consist of?

  • Clusters formed after bridge amplification
  • Short DNA sequences added to individual fragments
  • Glass slide with oligos that attach to adapters (correct)
  • Raw images processed into FASTQ files

    • What is the role of cluster in Illumina sequencing?

    <p>Formed after bridge amplification, multiple copies of the same DNA strand on flow cell</p> Signup and view all the answers

    What does base calling from raw data involve in Illumina sequencing?

    <p>Interpreting the identity of the base from the color of a cluster</p> Signup and view all the answers

    What is the format of FASTQ files in Illumina sequencing?

    <p>A txt file with four lines per read</p> Signup and view all the answers

    What is the significance of quality values in Illumina sequencing?

    <p>Represent the certainty of the base determined by the clarity of the spot on the flow cell</p> Signup and view all the answers

    What is the term for the rapid increase in frequency of a specific genetic variant due to positive natural selection?

    <p>Selective sweep</p> Signup and view all the answers

    Which of the following is a measure of the amount of genetic variation in a population?

    <p>Heterozygosity</p> Signup and view all the answers

    Which enzyme shears DNA at specific sites?

    <p>ApeKI</p> Signup and view all the answers

    Which allele is related to metabolism in bobcats, affecting energy expenditure and obesity?

    <p>GPR158</p> Signup and view all the answers

    Which allele is related to abdominal fat storage and lipid metabolism in bobcats?

    <p>LECT2</p> Signup and view all the answers

    Which allele is related to noxious heat detection in bobcats?

    <p>TRPM</p> Signup and view all the answers

    What is the term for distinct chromosomal regions where genetic variants are inherited together?

    <p>Linkage disequilibrium</p> Signup and view all the answers

    What does Fst measure in population genetics?

    <p>Divergence between populations</p> Signup and view all the answers

    What is the term for the process of identifying structural rearrangements in the genome?

    <p>CNVs</p> Signup and view all the answers

    What is the best Phred quality score indicating high consistency in DNA sequencing?

    <p>30</p> Signup and view all the answers

    Which method is suitable for de novo bacterial/viral genome assembly and BAC sequencing?

    <p>Pac bio (NGS)</p> Signup and view all the answers

    What does copy number variation (CNV) refer to?

    <p>Variation in repeated genome sequences</p> Signup and view all the answers

    What do string graphs in de novo assembly use to construct full sequence contigs?

    <p>Nodes representing reads</p> Signup and view all the answers

    What is the focus of transcriptome analysis?

    <p>RNA molecules in cells</p> Signup and view all the answers

    What is the method for SNP detection in genomes and can be used in genetic mapping and estimation of allele frequencies?

    <p>RADseq</p> Signup and view all the answers

    How are consensus sequences obtained from de novo assembly contigs based on?

    <p>Weighted voting, incorporating quality scores for accuracy</p> Signup and view all the answers

    What is the main purpose of genome re-sequencing?

    <p>To gather data on genetic variation through mapping reads to a known reference sequence</p> Signup and view all the answers

    What is the calculation of N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb?

    <p>30mb</p> Signup and view all the answers

    What is the purpose of large scaffolds in genomes with many repeats?

    <p>To be generated using mate pair libraries and methods that produce very long reads</p> Signup and view all the answers

    What are the cost-saving approaches for genome variation at the population level?

    <p>Low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment</p> Signup and view all the answers

    What is the main advantage of low/ultra-low coverage sequencing?

    <p>Data for the entire genome of multiple individuals and increased likelihood of detecting all alleles</p> Signup and view all the answers

    What does whole genome sequencing involve?

    <p>Sequencing the entire genome</p> Signup and view all the answers

    What should be considered for sequencing?

    <p>Capture amount, specificity, variability, reproducibility, cost, and input DNA</p> Signup and view all the answers

    Study Notes

    Advances in Genomic Sequencing Technologies and Strategies

    • Assembly using short reads combined with large mate libraries at different coverages helps assemble larger contigs
    • Comparisons between assembly programs should consider speed, error, number of contigs, and contig length
    • Velvet is a highly efficient genome assembly program for short DNA sequence reads
    • Genome re-sequencing aims to gather data on genetic variation through mapping reads to a known reference sequence
    • Structural variation analysis leverages the distance and orientation between paired reads to provide insights on genome structure
    • Bridge amplification is used in Illumina sequencing flow cells to amplify DNA fragments for sequencing
    • N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb is calculated as 30mb
    • Large scaffolds in genomes with many repeats can be generated using mate pair libraries and methods that produce very long reads
    • Whole genome sequencing involves sequencing the entire genome, while enrichment targets specific genomic regions
    • Cost-saving approaches for genome variation at the population level include low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment
    • Considerations for sequencing include capture amount, specificity, variability, reproducibility, cost, and input DNA
    • Advantages of low/ultra-low coverage sequencing include data for the entire genome of multiple individuals and increased likelihood of detecting all alleles

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    Description

    Test your knowledge about recent advances in genomic sequencing technologies and strategies with this quiz. Explore topics such as genome assembly, re-sequencing, structural variation analysis, sequencing platforms, and cost-saving approaches for population-level variation studies.

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