OMA browser: finding exact genome release information

Question

[olbei.marton]

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

Answer 1

[Adrian Altenhoff]

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the older bacteria - including your Salmonella strain - come originally from Expasy's GenomeReviews - a service that is no longer maintained.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

[olbei.marton]

Dear Adrian,

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

Best wishes, Marton