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?

Cellular location and process Signup and view all the answers

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

To find highly homologous sequences Signup and view all the answers

What do highly homologous sequences typically have?

Low E-values Signup and view all the answers

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

100 codons Signup and view all the answers

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

To find all ORFs 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?

Ribosome-binding site Signup and view all the answers

What is the purpose of gene prediction programs?

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

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

Putative protein-coding gene Signup and view all the answers

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

By searching for open reading frames in metagenomic data 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?

Open reading frame Signup and view all the answers

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

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

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

To verify the computer-generated gene assignments Signup and view all the answers

What is a coding sequence (CDS)?

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

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

To identify similarities and differences between sequences Signup and view all the answers

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

Genome curation Signup and view all the answers

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

Bioinformatics 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?

Putative protein of unknown function Signup and view all the answers

What is the purpose of genome curation?

To verify the accuracy of the predicted gene assignments 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?

Base-by-base comparison 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.