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Is there any existed tool for retrieving DBsnp from Blast output

Hi everyone,

So I have let's say a fasta file consists of 100 sequences.

1. I used Blastn to blast these 100 sequences and got the blast output.

2. I then parse the blast output. For each sequence, I know where the mismatch is comparing to the reference.

3. I want to search in dbsnp for each of the mismatches, if they exists or not.

So I don't know if there is such tool especially for locally search DbSNP data using these mismatch location information?

blast dbsnp variation alignment next-gen
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updated by Benn Benn • written by 309772486 • 309772486

1 answer

I think you miss a step in your approach. Like Pierre Lindenbaum is suggesting, you'll need to find genomic locations of your variants (or mismatches), probably in vcf format. Then you can annotate your variants (SNP) with known databases such as dbSNP.

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written by Benn Benn

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