The bioBakery help forum

How to annotate to the resistance gene database?

I want to annotate the data to resistance gene database(ARDB or CARD), how do I do it?
ARDB:https://ardb.cbcb.umd.edu/
CARD:https://card.mcmaster.ca/

Thanks!

What sort of data are you referring to? Sequencing reads? HUMAnN profiles?

Yes, I have some sequencing data from the metagenome. I learned that UniRef90 and UniRef50 gene families are available to the following systems:

  • MetaCyc Reactions
  • KEGG Orthogroups (KOs)
  • Pfam domains
  • Level-4 enzyme commission (EC) categories
  • EggNOG (including COGs)
  • Gene Ontology (GO)
  • Informative GO
    But I don’t know how to map to other databases,such as ARDB database.

I see what you mean. We don’t have ARDB-UniRef maps among the utility mapping files, that’s true. I’m not sure if it’s something that UniProt catalogs internally? In any case, you can build a custom mapping file for the regroup_table script by listing e.g. an ARDB familiy followed by a tab-delimited list of UniRefs, as in:

ARDB1<tab>UniRef1<tab>UniRef2<tab>UniRef3
ARDB2<tab>UniRef4<tab>UniRef5
ARDB3<tab>UniRef6<tab>UniRef7<tab>UniRef8
...

You would need to find the ARDB-UniRef relationships in either the UniProt or ARDB database OR determine them by homology (e.g. aligning ARDB proteins to the HUMAnN UniRef database with DIAMOND, for exampple).