Primer design shiny app

Tool:Primer design shiny app

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7.5 years ago

indiegene.blr ▴ 10

Here is a simple shiny app for designing primers for SNPs. It takes in genomic position (chr:start-end) and designs primers using primer3. It emails results to the user email address.

http://apps.indiegene.com/indiePrimer3/

It's currently working for hg19. We plan to add hg38 and in-silico PCR to test the uniqueness of the primers.

SNP sequencing • 2.1k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 7.5 years ago by indiegene.blr ▴ 10

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Is the source code for this available?

ADD REPLY • link 7.5 years ago by steve ★ 3.5k

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Looks nice, does it use a masked genome to avoid primers in repetitive elements?

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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It does avoid common repetitive elements. But it is specifically designed for SNPs and short indels and the product size is targeted to be around 1000bp. so if your repeats are longer than a few hundred bp, this is going to give no result right now.

ADD REPLY • link 7.5 years ago by indiegene.blr ▴ 10

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Could you add demo data ? seems it doesn't work for me .

ADD REPLY • link 7.5 years ago by sacha ★ 2.4k

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Thanks for trying. It takes in chr:start-end as input. For example, the rs5219 (the famous KCNJ11 SNP), the input should be chr11:17409572-17409572 or chr11:17409572-17409573.

Please note 'chr' prefix and the lowercase letters and no space between the coordinates. Of course, I can fix the upper case/ lower case thing.