I have a list of selected SNPs in which I am interested for genotyping. The conducting company needs the flanking sequence of each SNP ? How do I get this or how can I download it from NCBI Gene (it links me directly to the whole gene?)
I am looking forward for your answers
Do you have the SNP Ids in rs id form or u know their genomic positions? In case of rs id just go to the dbSNP and search your SNP ID it gives you the flanking seq too, or alternatively you can search in NCBI SNP open the search result it gives you a 51bp allele of SNP , BLAST this 51bp seq against nt/nr or ncbi genomes, open the best BLAST result add flanking seq by increasing/decreasing the limits of sequence.
If you have the genomic position and have many SNPs, you can use twoBitToFa from UCSC to fetch any flanking sequence you need. For only few of them you can just get them manually from the genome browser.
Hi Christina,
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. If you need more help on how to use BioMart, you can check out this tutorial from Ensembl: https://www.youtube.com/watch?v=QvGT2G0-hYA
HTH,
I like the answer provided by Kush, however, as he rightly mentions, you are limited to 50bp either side.
I guess a convenient and flexible solution is the following:
Go to the Genome Browser at genome.ucsc.edu
Search for your SNP either by rsid or position (both works)
At the top, in the drop-down menu, choose VIEW -> DNA
Under the Sequence Retrieval Region Options section add whatever flanking sequence length you like to either side.
The sequence is provided in a fasta format.
All the best.
You may want to try the Galaxy (https://usegalaxy.org/). Under "get flanking sequence" feature you may find what you need.
Cheers
You can follow these steps:
For the human genome hg19, I wrote a script that will convert a list of SNP rsIDs to a list of genomics positions in a bed format: chr, position, position+1 using quick MySQL table downloads from genome-mysql.cse.ucsc.edu (avoids ftp download of full data set and column selection).
https://github.com/milospjanic/rsID2Bed
Then, you can extend regions of a bed file, here is the code
http://www.genomicscode.org/2016/04/extend-range-of-bed-file-using-awk.html
Then, you can use bedtools and their module: bedtools getfasta to obtain a fasta sequence from a bed file.
I agree with Kush Shrivastava
You can get flanking sequence depending SNP ID (rsXXXX ) for aspecific SNP and mostly involve 50bp in addition to allele
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