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Is the COI sequence commonly used for DNA barcoding the sense or the antisense strand of DNA?

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  • $\begingroup$ You could use either with the same results. I imagine researchers would refer to the sense strand. $\endgroup$ – canadianer Nov 10 '17 at 21:04
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When the barcode sequence is generated by Sanger sequencing, it is sequenced in both strands, and presented in sense strand.

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  • $\begingroup$ Thank you very much for your answer, which I will accept. But it raises two further questions: 1) Is it always the case (at least for phylogenetics) that the sequence reported for a gene is the sense strand? (i.e. the strand which reads the same as the mRNA). 2) I was a bit confused when you said that both strands are sequenced in Sanger sequencing. I thought that just one of the complementary strands was sequenced? $\endgroup$ – Esteban Nov 11 '17 at 16:08
  • $\begingroup$ Careful workers ALWAYS sequence both strands, because some nucleotides are hard to read. Especially at the beginning and the end (the first 35 nucleotides or so, and anything out past 500 from the primers). So you sequence both strands so that one confirms the other. As one strand extends out past the easy to read "sweet spot", between 35 and 300 nucleotides from the primer, the other strand picks up with higher quality reads. Then you put the two together, carefully edit, and report the sense stand to GenBank. $\endgroup$ – Karl Kjer Nov 12 '17 at 13:24

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