How do I extract multiple primers from a sequence at once?

You can use the ToolsExtract Annotations operation to extract primers by setting ‘Match any of the following’ and then setting ‘Annotation type is primer bind’ and ‘Annotation type is primer bind reverse’.  This will create a separate primer document for each primer in your document table, and they will be available in your oligo database.  

Note that if you only want to extract individual primers from a sequence it is quicker to just select the primer annotation and click “Extract”.  This will extract the primer directly into oligo format.  

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  • Avatar
    Yejin Eun

    Hi I was able to use the Tools -> Extract annotation and got individual primers saved as a file, from a long sequence that had multiple primers in it.

    One issue is, however, that the primer annotation is now changed to "Binding Region" in each of the primer files. The title of the file is correctly labeled with the source sequence name and the original annotation, but the annotation within the primer file is just this generic binding region. Does this make sense, what I am describing? 

    Losing the specific annotation in each primer file is a problem because when I use the "Live Annotate and Predict" feature to search for existing primers in a new sequence, the ones that the software finds are just labeled as "Binding Regions" and do not say where they are from.



  • Avatar
    Yejin Eun

    I just found another bug. When I try to edit the annotation "Binding Region" that the software automatically put in, it does not allow me to edit the name. Also when I add a brand new annotation and give it a meaningful name, it will change it to "Binding Region" and ignore the name I gave it upon saving. 

  • Avatar
    Helen Shearman

    When you extract an annotated primer to create a primer document, the primer annotation is labelled "Binding Region".  This is to help distinguish the binding region of the primer from any 5' annotations on the primer as, if you run "Test with saved primers", only the annotated binding region is tested, not the 5' annotations. The primer document name is the original name of the primer annotation.

    The annotation is only labelled "Binding Region" when viewing the primer document.  When you run "Test with saved primers" and map the primer back to a sequence, the name of the annotated primer on the sequence is the name of the primer document (ie the original name of the annotation).

    However, if you use the "Find annotations" function (in the "Live annotate & Predict" tab) to map your primers to your sequence, the primer annotation is not renamed correctly.  The developers are looking into this further. Also note, that unlike the "Test with Saved Primers" function, the "Find annotations" function will only match the primer sequence to the sequence and will not recalculate the binding characteristics for the primer.