Prokka annotation _ with Pfam and TIGRfams databases

Dear all,

I am using PROKKA to annotate my bacterial assembly.fasta file

As I read in several discussions, PROKKA enables active annotation against HAMAP database of HMMs, but not Pfam and TIGRfams.

Is there any method to direct transfer the 2 databases, below, into galaxy, and use them in the annotation process?


Thank you,

Hi @Seraph


Not those specific files directly with Prokka. The first has a permissions problem (URL is incorrect?). The second could probably be used with other tools – search the tool panel at the EU servers for available choices. One example is PfamScan. Or, search the GTN tutorials with tool names or datatypes. Each has a listing of the public Galaxy servers that host a specific tutorial’s tools. Galaxy Training!

Note: Galaxy doesn’t modify the original underlying tool. Tools are instead “wrapped” in a way that makes it easier to use them all together all in one place: to build a workflow or to share exact methods/data with others. Or if you just prefer using a GUI :slight_smile:. The usage is (mostly) otherwise the same as the command-line.

Related: if you can find the fasta for other protein database sources, those can be included with Prokka using this option: Optional FASTA file of trusted proteins to first annotate from

Hope that helps!

thanks for the explanation