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Functional genomics has the goal of describing the functinos of all genes in a genome, including their expression and control of that expression. Functinal genomics incilves both molecular analysis in the laboratory and computer analysis of sequences(also called bioinformatics)
Sequence similarity searches to assign gene function
To assign gene function by computer analysis, the sequence of an unknown gene from one organism is compared to sequences of genes with know function in databases.
For the Unknown gene the sequence compared may be the DNA sequence of the gene itself or the amino acid sequence of the polypeptide encoded by the gene.
A sequence similarity search such as this may return a match for the whole sequence or part of it, the latter indicating that a domain of a gene's product has a known function.
Assigning Gene function experimentally
Gene function can be assugned experimentally by knocking out a gene or knocking down it's expression and investigating the phenotypes that result.
Different methods are used to knock out a gene, including replacing the normal chromosomal copy of the gene with a disrupted copy (used in many organisms) and inactivating the gene by inserting a transposon into it( typically used in bacteria).
The outcome in either case is a gene with no, or markedly reduced, function.
Gene knockouts made in this way are permanet changes in the chromosome.
Alternatively, gene expression can be silenced (KNOCKED DOWN) in many Eukaryotes at the translation level by RNA interference in which specific small regulatory RNA targets a specific mRNA for degradation.
This method DOES NOT cause permanet change, but prevents the translation of the mRNA of a target gene for as long as the small regulatory RNA molecule is present.
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