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Questions and Answers
What is the main purpose of a structured vocabulary in protein ontology?
What is the main purpose of a structured vocabulary in protein ontology?
What is used to measure the possibility of obtaining a sequence alignment by chance?
What is used to measure the possibility of obtaining a sequence alignment by chance?
What is a GO term based on?
What is a GO term based on?
What does a GO term define in addition to protein function?
What does a GO term define in addition to protein function?
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What is the purpose of comparing a query sequence to a database?
What is the purpose of comparing a query sequence to a database?
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What do highly homologous sequences typically have?
What do highly homologous sequences typically have?
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What is the minimum length of a sequence required to be considered a bacterial or archaeal ORF?
What is the minimum length of a sequence required to be considered a bacterial or archaeal ORF?
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What is the purpose of analyzing both strands of DNA in all three reading frames?
What is the purpose of analyzing both strands of DNA in all three reading frames?
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What is required at the 5' end of the gene for it to be considered a putative protein-coding gene?
What is required at the 5' end of the gene for it to be considered a putative protein-coding gene?
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What is the purpose of gene prediction programs?
What is the purpose of gene prediction programs?
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What is the term used to describe a protein-coding gene that has not been experimentally confirmed?
What is the term used to describe a protein-coding gene that has not been experimentally confirmed?
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How might metagenomics be used to isolate genes encoding a potentially new peptide antibiotic?
How might metagenomics be used to isolate genes encoding a potentially new peptide antibiotic?
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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?
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?
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What is the purpose of bioinformatics in the context of genomics?
What is the purpose of bioinformatics in the context of genomics?
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What is the primary goal of bioinformaticists when inspecting computer-identified genes?
What is the primary goal of bioinformaticists when inspecting computer-identified genes?
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What is a coding sequence (CDS)?
What is a coding sequence (CDS)?
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What is the purpose of comparing the sequence of predicted CDS with those in large databases?
What is the purpose of comparing the sequence of predicted CDS with those in large databases?
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What is the term for the process of verifying the computer-generated gene assignments?
What is the term for the process of verifying the computer-generated gene assignments?
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What is the primary field of study that combines biology, mathematics, computer science, and statistics?
What is the primary field of study that combines biology, mathematics, computer science, and statistics?
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What is the term for a region of DNA that appears to encode a protein but its function is unknown?
What is the term for a region of DNA that appears to encode a protein but its function is unknown?
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What is the purpose of genome curation?
What is the purpose of genome curation?
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What is the term for the process of comparing the sequence of two or more DNA or protein sequences?
What is the term for the process of comparing the sequence of two or more DNA or protein sequences?
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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.