ComputerLab2a_Goldberg_Feb3-2010

ComputerLab2a_Goldberg_Feb3-2010 - Ecological Genetics...

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Ecological Genetics Computer Lab 2 ECL242_PHR242 2/3/10 Lisa Goldberg Basics of Genotyping Collecting and proofreading raw genotype data from DNA Analyzer 1
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Analyzing genotypes on an agarose gel DNA Ladder allele “A” homozygous animals allele “B” Alleles “A” and “B” heterozygous animals +’s and –’s of agarose gel electrophoresis vs. capillary electrophoresis: * separation of alleles *multiplexing *cost * quality of image * specificity of bp calls * reagents * ease of interpretation * need of fluorescence 2 2000bp 50bp One Locus, 7 individuals 1000bp
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Analyzing Genotypes Electrophoretically Allele “A” Allele “B” Allele “C” Homozygous Animal Heterozygous Animal DNA ladder 3
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Fluorescent Dyes Four different fluorescent dyes can be used to detect alleles in an electropherogram PET (RED) NED (YELLOW) FAM (BLUE) VIC (GREEN) * NED shows up black on electropherogram Fluorescent dyes are added to the 5’ end of the forward primer The dyes allow detection of alleles within the capillary machine, as well as provide a way of distinguishing several loci within a multiplex reaction Note that some dyes are more robust than other. For example FAM usually works very well while NED can be tricky 4
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This note was uploaded on 03/02/2010 for the course ECL 242 taught by Professor Holly during the Winter '10 term at UC Davis.

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ComputerLab2a_Goldberg_Feb3-2010 - Ecological Genetics...

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