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,
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)
And you can also do the same with Ensembl BLAST.
Thanks! I will try that.
I run In Silico PCR as you said, but I am not sure how can I concatenate the results with SNP tracks (dbSNP)?
Ok I see it, sorry! Thanks for suggestion! Best, Agata
In the meantime I found another solution:
Download common SNPs from here: common_all.vcf.gz (https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/)
Define primer coordinates in genome.
Run samtools tabix common_all_vcf.gz chr:START-END
samtools tabix common_all_vcf.gz chr:START-END
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