how to retrieve a set of functions or functional categories (and/or the respective features) for a specific taxonomic group?

[Chintan Bhagat]

Dear all,

There is a large scale modification are made in MG-RAST. I like to download set of functions or functional categories (and/or the respective features) for a specific taxonomic group and also want to download set of taxonomic group for a specific functions or functional categories or retrieve a list of species or set of features linked to a specific functional category?

Can anyone guide me how to do it?

[Folker Meyer]

first: This is not the help desk... keep that in mind.

The analysis page supports this (AFAIK the manual has a section on it too). The basic idea is to use the filtering for e.g. Actinobacteria (using phylum level filter with e.g. RefSeq) and then select the function/categories you want. You can e,g, narrow it down to Subsystems (e.g. Lysine Biosynthesis) and then Export the fasta files (one of the tabs at the bottom of the page). All this is available on the analysis page.

You can of course also start with the function (e.g. filter for subsystem Lysine (  and then switch the view to Taxonomy (e.g. type=taxonomy) and view or export.

[Chintan Bhagat]

Thank you for your reply.

I did it serval time a few days ago, but not got any result.

However, I got the result just a day back in the same way as you said. 

Thanking You

Chintan Bhagat

[Folker Meyer]

we have added a video to our youtube MG-RAST channel about this. We refer to it as "slicing and dicing" (see: https://www.youtube.com/watch?v=hUwGzRNF6P8)

[Oscar Aguinaga]

Thanks for the video, very helpful. However, I can only perform "slicing and dicing" when using RefSeq database. It doesn't work with Silva or Greengenes. Is that expected?

[Folker Meyer]

yes this is expected as you can only analyze in one dimension (e.g. taxonomy) with the 16s ribosomal databases