are known polymorphisms in the primer sequence?
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2.7 years ago
agata88 ▴ 820

Hi all!

How can I check whether primer sequence include know polymorphisms?

I've read about snp blast, but it's seems no longer available: https://www.ncbi.nlm.nih.gov/SNP/snpblastByChr.html

Thanks for any suggestions,

Best, Agata

primer polymorphisms • 524 views
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2.7 years ago

A quite manual solution:

Assuming your genome is available in the UCSC genome browser you can use In silico PCR (go to Tools -> In Silico PCR). Add primer sequences, run the tool, and check if your primers overlap with known SNP tracks (dbSNP)

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And you can also do the same with Ensembl BLAST.

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Thanks! I will try that.

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I run In Silico PCR as you said, but I am not sure how can I concatenate the results with SNP tracks (dbSNP)?

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Ok I see it, sorry! Thanks for suggestion! Best, Agata

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2.7 years ago
agata88 ▴ 820

In the meantime I found another solution:

  1. Download common SNPs from here: common_all.vcf.gz (https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/)

  2. Define primer coordinates in genome.

  3. Run samtools tabix common_all_vcf.gz chr:START-END

Best, Agata

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