eggNOG - extracting orthologous sequences

Question

[urema]

Hi,

Basically I was wondering if anyone can give me the procedure for extracting orthologous protein sequences for my protein sequence of interest.

For example, I want to find all orthologs for protein P01112, say.

I can provide this sequence as input online and I get a result, however I want to know how one can use eggNOG offline, manually, by using the HMMs downloaded from eggNOG to then be used to find orthologs from eggNOG databases also retrieved from online.

I cant find a step-by-step guide for such thing on eggNOG or other sites.

Thanks, U.

[urema]

Nobody have any other insights ? Surely someone has even looked at eggNOG before ? If eggNOG is terrible or shouldn't or can't be used or anything, this would be great to know too. I am new to bio-informatics and I am not sure the best procedures etc. Textbooks have ortholog information etc. etc. but nothing on how to extract orthologs locally from eggNOG....

Answer 1

[Elisabeth Gasteiger]

I cannot reply for eggNOG, but as a side note: UniProtKB has cross-references to eggNOG and other phylogenomic databases. e.g. https://www.uniprot.org/uniprot/P01112#family_and_domains

You could pick an identifier from one of these cross-references and then query UniProtKB (also possible via the REST API http://www.uniprot.org/help/api) with such an identifier, e.g.

https://www.uniprot.org/uniprot/?query=database%3A%28type%3Aeggnog+KOG0395%29+&sort=score

https://www.uniprot.org/uniprot/?query=database%3A%28type%3Aorthodb+EOG091G0UAU%29&sort=score

Results can be downloaded in various formats, interactively or programmatically.

[urema]

I am new to the bioinformatics resources etc. I essentially want to get orthologous polymorphisms that exist for a particular protein.

So I assumed going down eggNOG route would be the procedure, then to use something like dbSNP/ensembl to get the polymorphisms.... Is Uniprot not for human proteins only, and the definition of orthologous proteins is a similar function in a different species?

Protein -> get orthologs -> get polymorphisms for these orthologs...

Thanks, U.

[Elisabeth Gasteiger]

Apologies for not replying sooner. As you have probably found out since you wrote this, UniProtKB is indeed not at all limited to human proteins, but currently holds sequences from more than 600,000 taxons, cf https://www.uniprot.org/taxonomy/?query=rank:species&fil=annotated%3Ayes&sort=score

You may also want to have al look at this help page: http://www.uniprot.org/help/orthologs_between_two_species

Please feel free to contact the UniProt helpdesk if you have any specific questions on UniProt.