Question: OMA browser: finding exact genome release information
0
gravatar for olbei.marton
4 months ago by
olbei.marton0 wrote:

Hi all,

I am really enjoying OMA, I managed to run it on a set of species I am interested in. I really appreciate that I can download the cDNAs directly from the website.

However, for some of my proteins I would be interested in looking at regulation as well, and I would need the non-coding parts of the genome.

My question is: where can I find the exact genome release the orthology was built from?

If I take a look at one of my species it lists the following:

  • UniProt identifier: SALA4
  • NCBI Taxonomy ID: 454166
  • DB Name: Salmonella agona (strain SL483) chromosome, complete sequence.
  • DB Release: 16-DEC-2008 (Rel. 100, Last updated, Version 3)

The answer is probably very obvious, but I have not worked with this kind of information before.

Best wishes,

Marton

orthology oma genome orthologs • 172 views
ADD COMMENTlink modified 4 months ago by adrian.altenhoff620 • written 4 months ago by olbei.marton0
2
gravatar for adrian.altenhoff
4 months ago by
Switzerland
adrian.altenhoff620 wrote:

Dear Marton,

generally speaking, the weblink on the genome page should direct you to the page from where we downloaded originally the genome.

Many of the older bacteria - including your Salmonella strain - come originally from Expasy's GenomeReviews - a service that is no longer maintained. The latest release of it is however still accessible via ftp: ftp://ftp.ebi.ac.uk/pub/databases/genome_reviews/last_release/dat/cellular/

If you need the exact genome we used in OMA, please contact us via email and the list of species you need - we do keep a copy of most of the source genomes.

As best alternative, you can go with the UniProt Reference proteome and check which assembly is linked to it.

Best wishes, Adrian

ADD COMMENTlink written 4 months ago by adrian.altenhoff620

Dear Adrian,

Thank you very much for your help. I will write an email with the requested source genomes.

Best wishes, Marton

ADD REPLYlink written 4 months ago by olbei.marton0
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