Question: Metagenomics functional annotation hmmsearch vs Blast ???
3
gravatar for David
2.5 years ago by
David160
David160 wrote:

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

blast hmm metagenomics eggnog • 1.3k views
ADD COMMENTlink modified 2.3 years ago by Manu Prestat3.9k • written 2.5 years ago by David160
5
gravatar for jhc
2.3 years ago by
jhc2.8k
Germany
jhc2.8k wrote:

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

ADD COMMENTlink written 2.3 years ago by jhc2.8k

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

ADD REPLYlink written 2.3 years ago by jhc2.8k
2
gravatar for Manu Prestat
2.3 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

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

ADD COMMENTlink written 2.3 years ago by Manu Prestat3.9k
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