What Is The Easiest Way To Obtain The Reference Sequence For All The Human Genome Snps.

Question

[User 0572]

Hello, I have very little background in bioinformatics (I'm a molecular biologist). I am trying to find the reference sequences of all the DB132 SNPs from the reference genome. Is there an easy way to obtain this information for someone unfamiliar with computer coding and bioinformatics?

[Jorge Amigo]

with reference sequences you really mean flanking sequences, or just the reference allele?

Answer 1

[Mikael Huss]

One simple way:

1. Go to the UCSC Genome Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start

2. Select the Variations and Repeats track in the "group" dropdown menu (after making sure that the genome dropdown manu says "human).

3. Select "Common SNPs(132)" in the track dropdown menu.

4. Click "Get output" (after checking that the "output format" menu has a suitable alternative like "all fields from selected table" selected).

Or:

Just download one of the SNP132 related files from ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

Answer 2

[Biogeek]

The UCSC Genome Browser allows you to input a genomic marker and downloading the sequence from a particular human genome assembly.

Here is an example

Was obtained by:

1. Searching for "DB132" in ucsc genome browser (http://genome.ucsc.edu/cgi-bin/hgGateway)
2. Right-clicking on the "RefSeq gene" track
3. Selecting "Gen DNA for DB132"
4. Clicking on button "Get DNA"

[User 0572]

I tried what you suggested, but I think the UCSC browser limits to only 1000 sequences.

Answer 3

[Mériem]

hello, i have the same problem here !! i tried your method but i couldn't find anything i'm looking for the rs number of a specific snp of the ACE gene that is ACE C1237T could i have some help please ???