Question: Download Strain-Specific Mouse Sequences
1
gravatar for Andrew Su
5.5 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 • 2.9k views
ADD COMMENTlink modified 5.5 years ago by Zev.Kronenberg11k • written 5.5 years ago by Andrew Su4.8k
2
gravatar for Zev.Kronenberg
5.5 years ago by
United States
Zev.Kronenberg11k wrote:

Here you go:

ftp://ftp-mouse.sanger.ac.uk/current_denovo

I found it under: http://www.sanger.ac.uk/resources/mouse/genomes/

"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 5.5 years ago • written 5.5 years ago by Zev.Kronenberg11k
1

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 5.5 years ago by Andrew Su4.8k
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