BMD427 Applied Bioinformatics Lecture 5: Genome Annotation Quiz
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Questions and Answers

What is the process of genome annotation?

  • Interpreting raw sequence data into useful biological information (correct)
  • Analyzing raw sequence data to identify repetitive elements
  • Creating raw sequence data from biological information
  • Mapping the location of genes in the genome

    • What is the main focus of genome annotation?

  • Determining the overall GC content of genomic DNA
  • Mapping the location of protein domains in the genome
  • Identifying the number of chromosomes in a species
  • Describing key features of genomic DNA (correct)

    • What is one of the key questions addressed in genome annotation?

  • What is the overall nucleotide composition of the genome?
  • How many chromosomes does the genome contain?
  • How long are the chromosomes in the genome?
  • What proteins do the genes encode? (correct)

    • What are some of the features described during genome annotation?

    <p>Repeats, promoters, and protein domains</p> Signup and view all the answers

    Why is genome annotation considered important?

    <p>To survey the landscape of genomic DNA and describe its key features</p> Signup and view all the answers

    What is known for many species regarding their genomic DNA?

    <p>The overall GC content varies between species</p> Signup and view all the answers

    What is a characteristic feature of eukaryotic genomes in terms of GC content?

    <p>GC content of about 35–45%</p> Signup and view all the answers

    What is a distinguishing feature of prokaryotic gene structure?

    <p>Polycistronic genes</p> Signup and view all the answers

    What is a key difference between eukaryotic and prokaryotic promoters?

    <p>Eukaryotic promoters are simple and located close to the gene</p> Signup and view all the answers

    What is a challenge in genome annotation according to the provided text?

    <p>Determining the location and structure of protein-coding genes</p> Signup and view all the answers

    Which type of gene prediction approach relies on similarity to other sequence types?

    <p>Extrinsic (homology-based)</p> Signup and view all the answers

    What is a characteristic feature of prokaryotic genomes in terms of gene density?

    <p>They are more densely packed with genes than eukaryotic genomes</p> Signup and view all the answers

    What is a defining feature of eukaryotic genes in terms of transcription?

    <p>Monocistronic genes</p> Signup and view all the answers

    What type of DNA distinguishes protein-coding DNA from non-coding DNA in the search by content gene prediction approach?

    <p>$GC$-rich DNA</p> Signup and view all the answers

    According to the text, what constitutes well over 50% of the DNA in a genome?

    <p>Repetitive elements</p> Signup and view all the answers

    What is a significant concern of genome annotation efforts, as mentioned in the text?

    <p>Identifying genes</p> Signup and view all the answers

    What is genome assembly?

    <p>The process of piecing together the DNA sequences of an organism's genome</p> Signup and view all the answers

    Why do short reads pose a challenge in genome assembly?

    <p>Short reads may be impossible to resolve repetitive regions</p> Signup and view all the answers

    What is a characteristic feature of genome complexity mentioned in the text?

    <p>High ploidy levels</p> Signup and view all the answers

    What do repetitive sequences in genomes do to assembly algorithms?

    <p>They can confound assembly algorithms</p> Signup and view all the answers

    Why is genome assembly considered crucial?

    <p>It provides a comprehensive representation of an organism's genetic diversity and evolution</p> Signup and view all the answers

    What is the primary challenge posed by heterozygosity in genome assembly?

    <p>Heterozygosity leads to inaccurate representations of the genome</p> Signup and view all the answers

    What can make assembly more difficult due to reads not always overlapping or matching perfectly?

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

    Which assembly method represents reads as nodes and overlaps between reads as edges in a graph?

    <p>De Bruijn Graph-based Assembly</p> Signup and view all the answers

    Which assembly method is efficient for short-read data and good for low to moderate complexity genomes but struggles with repetitive regions?

    <p>De Bruijn Graph-based Assembly</p> Signup and view all the answers

    Which assembly method is computationally intensive, slower, and better at handling repetitive regions?

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

    What do scaffolding algorithms aim to do after the initial assembly?

    <p>Create larger genomic segments (scaffolds)</p> Signup and view all the answers

    What type of genomes can make assembly more difficult due to reads not always overlapping or matching perfectly?

    <p>Heterozygous genomes</p> Signup and view all the answers

    Which factor can introduce errors in the reads, including base-calling errors, indels, and chimeric reads?

    <p>Sequencing Technologies</p> Signup and view all the answers

    Which assembly method uses pairwise read alignments to identify overlaps between reads?

    <p>Overlap-Layout-Consensus (OLC) Assembly</p> Signup and view all the answers

    Which assembly method is error-prone with long reads that can lead to misassemblies?

    <p>Overlap-Layout-Consensus (OLC) Assembly</p> Signup and view all the answers

    Which factor aims to improve the continuity and contiguity of genome assemblies by ordering and orienting?

    <p>Scaffolding algorithms</p> Signup and view all the answers

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