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Classical genetics works a little different than any other field of science. Primarily, instead of beginning with an hypothesis, geneticists try to deduce a conclusion based on inital observations and then later come up with hypotheses (and experiments to test the hypotheses). For example, maybe a geneticist is be interested in a certain area of developmental biology (let's say segmentation in Drosophila). They could mutagenize flys and then assay for changes in segmentation, which would indicate that genes involved in this process had been affected and new tools (loss- or gain-of-function mutants) are now available to study their functional roles in that process. The task would then be to work backwards from the phenotype to determine which gene caused it. Classical genetics = Phenotype -> Genotype. With the advent of whole genome sequences of several organism, scientists began identifying and manipulating candidate genes within an organism or candidate orthologs in another organism. eg. We know gene X plays a role in segmentation in Drosophila, what does the ortholog do in mice, Xenopus, Tribolium, etc.? or also, We know that protein X has certain characteristics, can we find potential genes that would produce a protein with similar characteristics? What is the functional importance of those gene?. Reverse Genetics = Genotype -> Phenotype. i.e. Quite literally reverse to what is normally (and still) done in classical genetics, this is how classical genetics is now sometimes referred to as forward genetics.
With the development of sophisticated molecular tools, the field of molecular genetics has emerged. Fundamentally, this addresses the consideration that genetics or molecular biology alone are not sufficient for a complete analysis of a system, the two must complement each other. For instance, if one can show that a given transcription factor activated Gene X by using genetic mutants, this can be more clearly defined by showing conclusively that the promoter region of gene X (when fused to a reporter construct) is activated in the presence of that transcription factor. Further, one can then mutate specific sites in this reporter region or reduce it to its essential sequence ("promoter bashing") to address its activation by the transcription factor in more detail. It is this meeting of genetics and molecular biology which is termed molecular genetics.
See also: Genetic linkage
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