Mapping files for KEGG, SEED, COG and Pfam classifications in MEGAN6


Report if the latest mapping files are not available


Hello everyone. I am new at MEGAN, and might have some basic doubts that I could not figured out by reading the manual.
One of them is related to this post of Rewati27. I just uploaded 9 metagenomic samples for analyzing at MEGAN6 (version 6.0.1 for MacOS). The samples were annotated against NCBI-nr database using BLASTX. I uploaded the rma files, although, I cannot access any of the functional annotations. KEGG, SEED, EggNOG, and other functional icons (of the toolbar) are all unactivated (B&W). I also can’t chose these database at the path " Change LCA parameter --> analyze using SEED; for example.
What should I do to proceed with functional annotations? Thanks



I have a more or less similar problem.
I want to analyse my BLAST-output with a comparison of the SEED database.
To do this I need a present RefSeq to SEED mapping file because I linked only 2 % of the BLAST-output with SEED.
Is it possible to create it by myself or can anyone give me a new version of the database?



Hi Amarots,

When you have BLASTX output files and want to create MEGAN RMA files with binning of reads into different functional classifications, you need mapping files. So these files have a mapping from the GI to KEGG, SEED, eggNOG classifications. MEGAN uses these mappings to bin reads into different functional classifications.

You can do the following:

  1. Download the mapping files from here:

  2. Unzip the mapping files.

  3. In the Import from BLAST dialog, for the tabs corresponding to each classification, choose the option “Load GI mapping file” and then load the corresponding mapping file that you downloaded and go ahead to create the RMA file.


Hi Rewati

I gather that the SEED mapping file needs to be downloaded from the MEGAN5 page. I would like to know if it is the extended version? If not, would you recommend extending it as mentioned in the MEGAN6 manual?