I want to calculate if a set of sequences of the internal transcribed spacer of a parasite are in Hardy-Weinberg equilibrium. I don´t know exactly how many copies does it have. My sequences have more than 200 polymorphic sites. How do I treat this data? Which software do you use?
Thanks in advance!
Just a reminder that H-W equilibrium is used to calculate whether ALLELES of one locus are in equilibrium. It is not used for multiple genes so I don't think it's a valid tool if you have multiple copies of your gene in the genome. You might be better off looking for mutation rates in the spacer region and if it is under selection pressure. Or see if there is a correlation between polymorphisms and geographic distribution and/or phylogenetic relatedness. Thought some ideas to consider.
Hello
Dose anyone know what protocol to use for crushing of tick before total genome DNA extraction?
Thanks in advance
Just a reminder that H-W equilibrium is used to calculate whether ALLELES of one locus are in equilibrium. It is not used for multiple genes so I don't think it's a valid tool if you have multiple copies of your gene in the genome. You might be better off looking for mutation rates in the spacer region and if it is under selection pressure. Or see if there is a correlation between polymorphisms and geographic distribution and/or phylogenetic relatedness. Thought some ideas to consider.
I think I agree with Katie. HW calculates if allele frequencies change from one generation to another. So might be difficult with multiple copies of the same gene. Perhaps you could try a Fisher's Exact test on the mutations testing for an expected number of heterozygotes. Heterozygote deficit or excess will suggest deviation from HW..
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