Genomics: Gene Naming and Ontology
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Questions and Answers

What is the main purpose of a structured vocabulary in protein ontology?

  • To define protein functions and cellular processes (correct)
  • To rank hits in decreasing similarity
  • To compare nucleotide sequences
  • To assign E-values to sequences
  • What is used to measure the possibility of obtaining a sequence alignment by chance?

  • E-value (correct)
  • GO term
  • Query sequence
  • Orthologous protein
  • What is a GO term based on?

  • Nucleotide sequence similarities
  • E-values of sequence alignments
  • Cellular locations of proteins
  • Amino acid sequence similarities among orthologous proteins (correct)
  • What does a GO term define in addition to protein function?

    <p>Cellular location and process</p> Signup and view all the answers

    What is the purpose of comparing a query sequence to a database?

    <p>To find highly homologous sequences</p> Signup and view all the answers

    What do highly homologous sequences typically have?

    <p>Low E-values</p> Signup and view all the answers

    What is the minimum length of a sequence required to be considered a bacterial or archaeal ORF?

    <p>100 codons</p> Signup and view all the answers

    What is the purpose of analyzing both strands of DNA in all three reading frames?

    <p>To find all ORFs</p> Signup and view all the answers

    What is required at the 5' end of the gene for it to be considered a putative protein-coding gene?

    <p>Ribosome-binding site</p> Signup and view all the answers

    What is the purpose of gene prediction programs?

    <p>To find genes that encode proteins or functional RNA products</p> Signup and view all the answers

    What is the term used to describe a protein-coding gene that has not been experimentally confirmed?

    <p>Putative protein-coding gene</p> Signup and view all the answers

    How might metagenomics be used to isolate genes encoding a potentially new peptide antibiotic?

    <p>By searching for open reading frames in metagenomic data</p> Signup and view all the answers

    What is the term used to describe a sequence of DNA that is not interrupted by a stop codon and has terminator sequences at the 3' end?

    <p>Open reading frame</p> Signup and view all the answers

    What is the purpose of bioinformatics in the context of genomics?

    <p>To predict genes that encode proteins or functional RNA products</p> Signup and view all the answers

    What is the primary goal of bioinformaticists when inspecting computer-identified genes?

    <p>To verify the computer-generated gene assignments</p> Signup and view all the answers

    What is a coding sequence (CDS)?

    <p>A region of DNA that appears to encode a protein</p> Signup and view all the answers

    What is the purpose of comparing the sequence of predicted CDS with those in large databases?

    <p>To identify similarities and differences between sequences</p> Signup and view all the answers

    What is the term for the process of verifying the computer-generated gene assignments?

    <p>Genome curation</p> Signup and view all the answers

    What is the primary field of study that combines biology, mathematics, computer science, and statistics?

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

    What is the term for a region of DNA that appears to encode a protein but its function is unknown?

    <p>Putative protein of unknown function</p> Signup and view all the answers

    What is the purpose of genome curation?

    <p>To verify the accuracy of the predicted gene assignments</p> Signup and view all the answers

    What is the term for the process of comparing the sequence of two or more DNA or protein sequences?

    <p>Base-by-base comparison</p> Signup and view all the answers

    Study Notes

    Gene Annotation and Naming

    • A structured vocabulary called ontology is used to define how new genes and proteins are named.
    • The standard gene ontology (GO) is used to name proteins, motifs within proteins, and their functions.
    • GO terms reflect protein function, cellular process, and cellular location.

    Sequence Comparison and Alignment

    • Programs compare the nucleotide or amino acid sequence of a query sequence to all other sequences in a database.
    • The results, or "hits," are ranked in order of decreasing similarity.
    • Each alignment is assigned an E-value, which measures the possibility of obtaining the alignment by chance.
    • Highly homologous sequences have very low E-values.

    Orthologues and Paralogues

    • Orthologues are proteins with similar sequences and functions in different species.
    • Paralogues are proteins with similar sequences but different functions within the same species.

    Conserved Hypothetical Proteins and Putative Proteins

    • A conserved hypothetical protein is a protein with a conserved sequence but unknown function.
    • A putative protein of unknown function is a protein predicted to exist based on sequence analysis but without functional annotation.

    Genome Curation and Annotation

    • Bioinformaticists manually inspect computer-generated gene assignments to verify their accuracy.
    • This process is called genome curation.
    • Putative open reading frames (ORFs) are analyzed to identify potential protein-coding genes.
    • ORFs are recognized as sequences of at least 100 codons that are not interrupted by stop codons and have terminator sequences at the 3' end.

    Physical Genome Map Construction

    • Bioinformaticists develop algorithms to compare predicted coding sequences with those in large databases.
    • The base-by-base comparison of two or more sequences helps to identify potential genes.

    Open Reading Frames (ORFs) and Gene Prediction

    • ORFs are potential protein-coding genes recognized by gene prediction programs.
    • Programs identify ORFs by analyzing both strands of DNA in all three reading frames.
    • A bacterial or archaeal ORF is defined as a sequence of at least 100 codons that is not interrupted by a stop codon and has terminator sequences at the 3' end.

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    Description

    This quiz covers the process of comparing query sequences to database sequences and the importance of standard gene ontology in genomics.

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