Question: Download Strain-Specific Mouse Sequences
gravatar for Andrew Su
5.0 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

A colleague asked me a simple question for which I've yet to find a simple solution. The FASTA files for many mouse strains have been sequenced and assembled. He'd like to download the sequence of a given gene in a specific strain (e.g., TP53 in A/J). That Sanger page provides easy tools to look at variation, but I just want a plain FASTA file. I was hoping there would be a BioMart instance but no luck, and the main BioMart Central doesn't appear to have anything relevant.

I'm still hoping there's a user-friendly web tool out there that I'm just missing. If not that, then a bioinformatics solution that is easier than creating a BLAST database, blasting B6 sequences to get coordinates, and then fastacmd to get subsequences. Solutions for the lazy bioinformatician are appreciated!

genome mouse download • 2.7k views
ADD COMMENTlink modified 5.0 years ago by Zev.Kronenberg11k • written 5.0 years ago by Andrew Su4.8k
gravatar for Zev.Kronenberg
5.0 years ago by
United States
Zev.Kronenberg11k wrote:

Here you go:

I found it under:

"Denovo Assemblies in FASTA format" half way down the page

I hope you find this to be the path of least resistance.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Zev.Kronenberg11k

Hi Zev, thank you, yes, I found that link. However, those FASTA files are chromosomal assemblies, one sequence per chromosome. I was hoping for a way to extract the sequence for a specific gene. I can do it with those FASTA files (create BLAST database, BLAST B6 sequence, then extract coordinates), but I was hoping there was a more efficient way... wishful thinking maybe?

ADD REPLYlink written 5.0 years ago by Andrew Su4.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 609 users visited in the last hour