nucleotide blast of flanking sequences around SNPs
2
1
Entering edit mode
4.2 years ago

Hi, I have some SNPs with flanking sequences ~60 kb both upstream and downstream of a SNP. The flanking sequence looks some thing like this. ATTATGGCT[A/T]TTAGCTTA (this is just an example). My question is 1) I am making my own fasta file by using this information and converting aforementioned sequence as snp_c1 ATTATGGCTATTAGCTTA and doing blast. I am keeping ref allele only and in this case it is A. So is this a correct way of adding flanking sequence info to query or should I make a fasta file like this and do BLAST? snp_c1 ATTATGGCTATTAGCTTA (this is flanking sequences with ref allele) snp_c1 ATTATGGCTTTTAGCTTA (this is flanking sequence with alt allele)

2) Second thing whats the best way to filter blast hits? I am keeping only unique hits but I am confused about the optimal thresholds that I can apply on bit score and e-value? Is there any threshold to do filtering when it comes to SNP's?

SNP nBLAST • 1.3k views
ADD COMMENT
2
Entering edit mode
4.2 years ago

If you have the genomic locations of the SNPs, you can get upstream and downstream flanking regions using BioMart at Ensembl. Just use region section in filters to write in your SNPs, and select the upstream and downstream flank options in the sequence section of attributes.

ADD COMMENT
0
Entering edit mode
4.2 years ago

How to use BioMart tutorial:

ADD COMMENT

Login before adding your answer.

Traffic: 3753 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6