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Old 11-17-2011, 12:19 PM   #3
Simcom
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Location: East Coast US

Join Date: Jun 2010
Posts: 8
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I am sequencing viral DNA/gDNA integration junctions, so I am using that 5 nucleotides of viral DNA as a type of 'verification', that indeed a read contains the junction between viral DNA and gDNA, essentially showing that the sequencing primer is not mis-hybridizing to a similar (non-viral) sequence elsewhere in the genome. We are using a custom sequencing primer, but we prefer that it not hybridize up the the very edge of the viral DNA for reason described above.
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