SNPcheck alternative

Question

[KirGen]

Hi,

I always use SNPcheck tool to see if primers that I need have SNP that occurs within them. This tool hasn't worked for days, I don't Know if this service is due to close. Is anybody aware of any alternative tool that could perform this function?

Thanks a lot!

[Pierre Lindenbaum]

https://www.reddit.com/r/bioinformatics/comments/8qsh48/snpcheck_alternative/

My lab uses SNPcheck 3.0 (link) to check 1000s of primers to see if a previously reported SNP occurs within them. However, this service is due to close down soon. Is anybody aware of any alternative tool that could perform this function? Things like BLAST and Primer3 can you be used for a one-at-a-time approach but we process primers in large batches

[KirGen]

I have tried to use them but I didn't find informations about SNP that could interest my primers. Do you know where I can find informations about SNP in these tools? Thanks

[Pierre Lindenbaum]

Do you know where I can find informations about SNP in these tools? Thanks

ncbi dbsnp => download

[KirGen]

Ok thanks, but there isn't the possibility to put the sequence of the primer of interest inside this tools (as for snp check) and to see if there are snp in the primer and where are them?

[GenoMax]

You could try UCSC's in-silico PCR tool, if your genome of interest is available there: https://genome.ucsc.edu/cgi-bin/hgPcr