Mouse Gene Annotation Table

[carmeyeii]

Hi all,

I am writing a script to figure out which genes [in the whole genome] are the closest to each one in my list of "interesting" genes. I have a list of "interesting genes", as well as their start and end positions, but I need a list that contains ALL the annotated genes in mus musculus, along with their start and end positions.

Can somebody point me in the right direction?

I have only found the MGI [Mouse Genome Informatics] table found here :

ftp://ftp.informatics.jax.org/pub/re...Coordinate.rpt

But I don't know if this is the standard file of all mus musculus genes and their positions -- certainly there must be a "standard" file such as a GTF or something from RefSeq or Ensembl, no?

Thank you so much,

Carmen

[carmeyeii]

Just bumping it up in case anyone here is mouse-saavy.

Thanks!

[carmeyeii]

Anyone?

[GenoMax]

You can find the GTF file for mouse from ensembl here: ftp://ftp.ensembl.org/pub/release-69/gtf/mus_musculus/

Annotated genbank format sequences here: ftp://ftp.ensembl.org/pub/release-69.../mus_musculus/

[swbarnes2]

You can get mouse gene start and stop info from ensembl.

With two bed files, you can use closestBed from BEDTools to figure out which whole gene is closest to your interesting gene