This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: Primer design shiny app

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
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updated by Ram Ram • written by indiegene.blr • indiegene.blr

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

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written by WouterDeCoster WouterDeCoster

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.

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written by indiegene.blr • indiegene.blr

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

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written by sacha sacha

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.

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written by indiegene.blr • indiegene.blr

Is the source code for this available?

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written by steve steve

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