Metagenomics functional annotation hmmsearch vs Blast ???

Question

[David]

Hi, I have run a metagenomics shotgun project and after assembling and binning my contigs i have predicted the genes using prodigal. I have both nucl and protein sequences.

The next step is to predict the functional annotation of my bins and i need some advice on how to proceed.

My first idea is to use the eggnode database, specifically their hmm models and align my predicted proteins to their hmm models using hmmsearch.

I have also seen people running blastp or diamond on eggnog protein files.

What do you think ??

Thanks for advice, David

Answer 1

[jhc]

eggNOG just released eggnog-mapper, a tool for (meta)-genome functional annotation:

[jhc]

related: Method description and benchmark comparison against BLAST, interPro and CAFA2 https://doi.org/10.1093/molbev/msx148

Answer 2

[Manu Prestat]

There is also this hmm db: http://cbb.pnnl.gov/portal/software/FOAM.html (for which, I should say, I was a bit involved).