Question
In most mammalian genomes, the dinucleotide CpG (that is, a C next to G on a single strand of DNA) is generally underrepresented relative to
In most mammalian genomes, the dinucleotide CpG (that is, a C next to G on a single strand of DNA) is generally underrepresented relative to expectation. If the overall genome frequency of cytosine and guanine is fC=0.3 and fG=0.3, at what frequency would you expect to find the CpG dinucleotide, assuming the genome is composed of bases in random order?
If you observed N CpGs out of a genome of length L bases, how might you determine whether the observed N is significantly underrepresented relative to expectation? Detail all steps you would take through to your final decision of being underrepresented or not.
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