How do I reverse complement primers?

Primers are always 5’ to 3’ so in Geneious if you reverse complement a primer, the sequence viewer will show the other strand and the primer direction arrow will switch from left to right to right to left. In the text view you should see that the primer hasn’t actually changed and is still the original sequence. If you really want to switch the primer to the other strand it needs to be run through ’Characteristics for Selection’ again since the annotated primer now doesn’t correspond to the sequence. It is worth deleting the current primer annotations and then running the ’Characteristics for Selection’ tool, which will create a new primer annotation running from left to right that corresponds to the sequence as it now exists.

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Comments

  • Avatar
    Bruce Sodowich

    This isn't working for me.  I can't get the Geneious to give me the reverse complement of my primer of interest.  I have used the Characteristics for Selection tool several times on the same selection and I still get the same orientation.  Can you be more specific here?   I have also sent an email about this.

     

    Thanks.

  • Avatar
    Helen Shearman

    Have you reverse complemented the primer first (ie selected the primer document and clicked the "R.C." button) before running "Characteristics for Selection"?  The "Characteristics for Selection" tool does not change the orientation of the sequence.