Hello, Im working on a metagenomic analysis where I need a reference set consisting of ~1500 prokaryotic genomes (in fasta format) from MetaHit and GenBank. My aim is to annotate the genes in this genomes with eggNOG orthologous groups.
From the eggNOG download site I think the dataset "Bacteria non-supervised orthologous groups (bactNOG) and their proteins" seems suitable for my annotation (flatfile).
The dataset looks like this:
## Protein name start_position end_position orthologous_group orthologous_group description
9685.ENSFCAP00000011039 1 363 meNOG04000 Leucine-Rich repeat protein SHOC-2
7159.AAEL014718-PA 5 527 meNOG04000 Leucine-Rich repeat protein SHOC-2
9606.ENSP00000352411 1 582 meNOG04000 Leucine-Rich repeat protein SHOC-2
7719.ENSCINP00000009123 9 531 meNOG04000 Leucine-Rich repeat protein SHOC-2
My question is: How I can perform this annotation, how I can annotate my set of prokaryotic genoms with this informations? Or I need also take into account the file "Protein sequences of all species, with the eggnog protein name."?
Thank you!
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munch •
1 answer
I imagine that this data already exists somewhere for the MetaHit sequences as the Bork group, who did the bioinformatic analysis of the MetaHit sequences, used eggNOG n their pipeline. see SmashCommunity: a metagenomic annotation and analysis tool and their website: http://www.bork.embl.de/software/smash/. You'll could use the same approach on the genbank sequences.
I suggest you contact Peer's group if you want to know where to access the MetaHit annotations and/or if you need help with using their pipeline.
Hope this helps Sarah
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