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Draw PCR primer locations


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4 replies to this topic

#1 thekid

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Posted 24 March 2009 - 12:29 PM

Hello,


I would like to know if there is any tools that can be used to draw PCR primer locations against a reference strain. I am comparing 15 sets of primers and it would be easier if I could just type in the location of each primer and it shows on the drawing instead of manually doing it using microsoft word.

Please let me know if there is any tool available.

thekid

#2 pcrman

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Posted 24 March 2009 - 06:29 PM

If you have Vector NTI..., probably not.

If you know how to use UCSC genome browser, you can add your primer sequences as customer track, the browser will aling the primer sequence to their target on the genome. Once you get your primers aligned with your genes, you can click the PDF/PS click at the top to export the graph into PS format which you can further manipulate in illustrator to generate publishable figures. It is very powerful.

#3 thekid

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Posted 24 March 2009 - 07:05 PM

Hello,

Thank you for the information, yes I do not have access to vector nti. Does the UCSC have options for virus genome or is it only selected genome.


thekid

#4 pcrman

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Posted 24 March 2009 - 08:20 PM

sorry UCSC doesn't have viral genome. If you know Perl you can use bioperl to draw the primers on a sequence, otherwise, you have to do it in word or illustrator.

#5 bglick

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Posted 28 April 2012 - 09:00 AM

SnapGene Viewer is free for Mac and Windows, and it has a great interface for displaying primers aligned to a reference sequence:

http://www.snapgene....napgene_viewer/




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