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Primers that do not align at regions with SNPs. Where to find SNPs?


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2 replies to this topic

#1 susanna

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Posted 16 July 2010 - 05:21 AM

Hi,

I was making primers, based on the genomic sequence of a gene.
Therefore, I wanted to check if my primers are not situated at regions with SNPs.
To accomplish this, i'm searching for an overview of SNPs in the gene.
Can anyone tell me, were i can find an overview of SNPs in the genomic sequence of genes?

thank u,

Susan

#2 Michaelro

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Posted 16 July 2010 - 10:33 PM

Hi
We use UCSC genome browser
http://genome.ucsc.e...hgsid=165533714
After finding your sequence of interest, choose SNP assembly options in Variation and Repeats section (130 should be most updated but it is worth looking on SNP129 too).Then Press Refresh button.
Hope it helps
Best
Michael

Hi,

I was making primers, based on the genomic sequence of a gene.
Therefore, I wanted to check if my primers are not situated at regions with SNPs.
To accomplish this, i'm searching for an overview of SNPs in the gene.
Can anyone tell me, were i can find an overview of SNPs in the genomic sequence of genes?

thank u,

Susan



#3 susanna

susanna

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Posted 20 July 2010 - 02:05 AM

thank u!

Hi
We use UCSC genome browser
http://genome.ucsc.e...hgsid=165533714
After finding your sequence of interest, choose SNP assembly options in Variation and Repeats section (130 should be most updated but it is worth looking on SNP129 too).Then Press Refresh button.
Hope it helps
Best
Michael

Hi,

I was making primers, based on the genomic sequence of a gene.
Therefore, I wanted to check if my primers are not situated at regions with SNPs.
To accomplish this, i'm searching for an overview of SNPs in the gene.
Can anyone tell me, were i can find an overview of SNPs in the genomic sequence of genes?

thank u,

Susan






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