are known polymorphisms in the primer sequence?

Question

[agata88]

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

Answer 1

[WouterDeCoster]

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)

[Jean-Karim Heriche]

And you can also do the same with Ensembl BLAST.

[agata88]

Thanks! I will try that.

[agata88]

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

[agata88]

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

Answer 2

[agata88]

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