(of note, all exons are ORFs, but not all ORFs are exons). ORFs are usually
detected using ab initio approaches.
• Coding sequences (CDSs) – A CDS is an exon or series of exons that make up the
protein coding portions of a mature mRNA. CDSs are usually identified by
sequencing of cDNAs and homology-based alignment of cDNAs with a genome
sequence. However, ab initio approaches have also proven useful in
identifying CDSs.
• Introns – Sequences between the exons within a gene.
• Promoters – Sequence upstream from, and relatively near, an ORF.
• Mobile elements (MEs) – Sequences with motifs and features characteristic of
one of the many types of mobile elements. Mobile elements are often initially
detected by homology-based comparisons with known MEs followed by ab initio
scans.
• Tandem repeats including microsatellites (SSRs).
• miRNAs.
Initial computer-based annotation may be further refined manually.
3.28 Functional Annotation
Functional annotation is assignment of biological data to structurally annotated
genome features. Functional annotation may include information about gene function,
biochemistry, interactions, expression, and regulation. The assignment of function to a
gene is ultimately dependent upon experiments that show how the absence or reduced
expression of that gene affects phenotype. Alternatively, biochemical experiments that
demonstrate the role of a gene product in a particular metabolic pathway may be used to
determine a gene’s function (although genes may have multiple functions). The former
groups of experiments, often known as “functional genomics” approaches, are relatively easy to perform in Arabidopsis but are more difficult in other plants. Consequently, for newly sequenced plant genomes, gene function may be tentatively
assigned to a gene based upon the function of its Arabidopsis (or other plant species)
ortholog (if one exists). Because highly similar gene sequences may have very different
functions in vivo, functional annotation not directly based on experiments done in the
species whose genome is being annotated should be treated with great caution.
The Gene Ontology (GO) Consortium has worked to develop a controlled,
standardized vocabulary for use in assigning functional annotations to genes. Even
if the function of a gene is unknown, GO annotation helps place the gene into one of
several larger categories based upon its domains and/or the functions of its orthologs.
At the highest GO level, genes are categorized as either cellular component, molecular function, or biological process.
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detected using ab initio approaches.
• Coding sequences (CDSs) – A CDS is an exon or series of exons that make up the
protein coding portions of a mature mRNA. CDSs are usually identified by
sequencing of cDNAs and homology-based alignment of cDNAs with a genome
sequence. However, ab initio approaches have also proven useful in
identifying CDSs.
• Introns – Sequences between the exons within a gene.
• Promoters – Sequence upstream from, and relatively near, an ORF.
• Mobile elements (MEs) – Sequences with motifs and features characteristic of
one of the many types of mobile elements. Mobile elements are often initially
detected by homology-based comparisons with known MEs followed by ab initio
scans.
• Tandem repeats including microsatellites (SSRs).
• miRNAs.
Initial computer-based annotation may be further refined manually.
3.28 Functional Annotation
Functional annotation is assignment of biological data to structurally annotated
genome features. Functional annotation may include information about gene function,
biochemistry, interactions, expression, and regulation. The assignment of function to a
gene is ultimately dependent upon experiments that show how the absence or reduced
expression of that gene affects phenotype. Alternatively, biochemical experiments that
demonstrate the role of a gene product in a particular metabolic pathway may be used to
determine a gene’s function (although genes may have multiple functions). The former
groups of experiments, often known as “functional genomics” approaches, are relatively easy to perform in Arabidopsis but are more difficult in other plants. Consequently, for newly sequenced plant genomes, gene function may be tentatively
assigned to a gene based upon the function of its Arabidopsis (or other plant species)
ortholog (if one exists). Because highly similar gene sequences may have very different
functions in vivo, functional annotation not directly based on experiments done in the
species whose genome is being annotated should be treated with great caution.
The Gene Ontology (GO) Consortium has worked to develop a controlled,
standardized vocabulary for use in assigning functional annotations to genes. Even
if the function of a gene is unknown, GO annotation helps place the gene into one of
several larger categories based upon its domains and/or the functions of its orthologs.
At the highest GO level, genes are categorized as either cellular component, molecular function, or biological process.
146
D. G. Peterson and M. Arick