Hi Shashank (and others),

I believe I know an answer for the question, but it may be not the easiest way to do it. ;)

Being here: http://metagenomics.anl.gov/metagenomics.cgi?page=KeggMapper

You can expand 'Metagenomes section', pick the one you are interested in and then click 'load data' below. You can load one more, as Data B (change at the top).

On the right, just above the graphics, there is a button 'export kegg abundance'. After you click it, new window will show - with the abundances you searched for. It is possible to save them from there ('Click to save as tab-delimited text file' at the top).

I hope this helped. ;)

Kind regards,
Marta

I am here to dig the tomb.

You can go to "Metagenome Analysis" page and select the metagenome you're interested in. Then you can choose the annotation method and database, let's say, "Functional Abundance" →"Hierarchical Classification"→"Annotation source"=KO

Now you can generate the table and get the annotation/gene abundance, and download this table if necessary.

Hope this would help.