Get KEGG Orthology entries from metagenomic data

[almicach]

Hi, I am would like to get KOs from metagenomic data, I am using the script:

perl mebs.pl -input dir_metagenomic -type metagenomic -comp

I get a table with Pfam ids, entropy, and #matched_peptides, but not KOs. I guees I need to use --keggmap parameter but I don´t no how

Could you help me, please?

[valdeanda]

Hi Ale,
The current mess v1.2 only have the correspondences of nitrogen and sulfur cycle (however if you have your correspondences for the other cicles you can add them too). When you compute the scores, in your input directory with metagenomees there should be a *.sulfur.score and *.nitrogen score file. At the end of those files you should see something like this

# Script to map these Pfam domains in KEGG->User Data Mapping.
# Colors are proportional to the number of Pfam matches and normalized with respect to the max.
# Note that a reference map must be selected first. For instance, Sulphur metabolism is:
# http://www.genome.jp/kegg-bin/show_pathway?map00920
# WARNING: note that several K numbers might map to the same protein.
# These cases are coloured in KEGG with the color of the last given K number.
# You might want to manually adjust the colors to correct this.
K00111 #abd9e9,black
K00112 #ffffbf,black
K10831 #d7191c,black
K11181 #fdae61,black
K13991 #2c7bb6,black
K15372  #2c7bb6,black

So in order to visualize them with KEGG, go to the corresponding metabolic pathway.. in this case sulfur metabolism map00920 and on the left corner in the 'Colors" tab, copy and paste those entries to visualize them

Let me know if that worked!
Best
Val

[almicach]

Thanks for the answer, Val. I followed your instructions and now I can visualize my results in pathway maps.