Question: Using Eggnog-mapper to categorize genes according to OG, without gene prediction.
0
gravatar for Hansen_869
3 months ago by
Hansen_86920
Hansen_86920 wrote:

Hi! I have recently used Prokka on a set of bins, to annotate their genes. In order to make the dataset of annotated genes more manageable, I'd like to categorize all the genes, according to their function. I haven't decided, how narrow the categorization should be yet. I have been told that EggNOG-mapper should be able to do this, however, when i read about EggNOG, it looks like it also annotates genes. As that would be double work, I'd like to ignore that function and only categorize the already annotated genes. Is this possible? Or am I better off not running Prokka and just use EggNOG? (Maybe I'm wrong, but I have had a hard time interpreting their github page).

Thanks!

annotation prokka eggnog • 294 views
ADD COMMENTlink modified 3 months ago by Carambakaracho2.0k • written 3 months ago by Hansen_86920
0
gravatar for Carambakaracho
3 months ago by
Carambakaracho2.0k
Germany/Cologne
Carambakaracho2.0k wrote:

the eggnog mapper does no ab initio prediction, it annotates provided genes/proteins. You'll get additional annotation to the one prokka offers and can categorise based on that.

ADD COMMENTlink written 3 months ago by Carambakaracho2.0k

Ah that makes more sense! So all I have to provide to EggNOG, is the protein sequence file (.faa) from the Prokka output? The reason why I'm asking and not trying, is due to the vast databases I have to download. If EggNOG is not right, it would be a lot of work for nothing.

ADD REPLYlink written 3 months ago by Hansen_86920

I used the diamond database for a quick shot and then refined with more specific databases

ADD REPLYlink written 3 months ago by Carambakaracho2.0k

Whats the difference between HMMER and Diamond?

ADD REPLYlink written 3 months ago by Hansen_86920

DIAMOND- Accelerated BLAST compatible local sequence aligner https://github.com/bbuchfink/diamond
HMMER - biosequence analysis using profile hidden Markov models http://hmmer.org/

ADD REPLYlink written 3 months ago by genomax78k

Thanks!! So they seem kind of similar. Why would I use one over the other?

ADD REPLYlink written 3 months ago by Hansen_86920

the hmmer version gave me more results, as far as I recall. Diamond was way faster though

ADD REPLYlink written 3 months ago by Carambakaracho2.0k

I am currently using EggNOG with diamond now. My file is about 2MB. As of now, diamond has been running for 50 minutes with no results (on 4 cores). Do you recall if this is the usual time, or might there be an issue?

ADD REPLYlink written 3 months ago by Hansen_86920

Depends what database you are running against?

ADD REPLYlink written 3 months ago by genomax78k

My shell command looks like this: python emapper.py -i input-file --output output-file -m diamond.

It states that when using diamond, no database should be specified on EggNOGS github.

ADD REPLYlink written 3 months ago by Hansen_86920
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