What is eggnog better than previous annotation in terms of?

Question

[Riku]

Hi, all.

I used eggnog to get annotations in de novo RNAseq analysis But I haven’t understand the merit. What is eggnog better than previous annotation(ex. BLAST etc.) in terms of?

Although I had read ths instruction in eggnog, I hadn't understand clearly. Why do we get accurate annotations using ortholog with eggnog?

Sorry for my basical question. I really appreciate in advance!

Answer 1

[lieven.sterck]

well, there are two aspects in play. One is the quality of the annotations you get, the other is the quantity . eggnog, or using orthology, to transfer protein function from one species/protein to another is far more accurate then simply using blast as we are much more certain those proteins will have the same function (being orthologous) then simply share a certain level of idenity/similarity.

If you use blast for instance you will get an 'annotation' for far more proteins but what you get will be less accurate or informative.

The really basis is that we assume that orthologus genes will have most likely retained their original biological function. But do consider this a very very brief explanation, as this is a while field of study in biology and several exceptions and such exist.

[Dunois]

Isn't EggNOG (or at least eggnog-mapper) simply doing a sequence search internally anyway?

[lieven.sterck]

very well possible (don't know the specifics of EggNOG) but I'll also assume it will do some more with it and the similarity search is merely the beginning.

I must also admit I was more answering the 'using orthology' part of the question than the eggnog specific case.

[Riku]

Thank you for your explanation!

Do you mean that eggnog not only performs sequence homology research, but also guesses orthologs from the results and obtains annotations associated with them?

By the way, sorry for my late reply. Thank you.

[lieven.sterck]

As said, I'm not familiar with the details of eggNOG but I would assume something like that indeed.

[Riku]

I got it. I understood this very easily.

Thank you very much for your kind explanation!