This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Metagenomics functional annotation hmmsearch vs Blast ???

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

eggnog hmm metagenomics blast
• 4,617 views • link
updated by Manu Prestat Manu Prestat • written by David David

2 answers

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

• 0 views • link
written by jhc jhc

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

• 0 views • link
written by Manu Prestat Manu Prestat

Log in to answer this question.

More posts like this