PhiSpy training set script

[cgr....@gmail.com]

Hi,
I would like to use PhiSpy to find prophages in some weird Archaea. I would like to generate training sets for these. Can I get a script for this?
Thanks
Chris Brown (Otago University)

[Kate]

We do not currently have a script to make your own training set, however we are planning a cumulative overhaul of PhiSpy in the near future.  This would include remaking the training sets.  In the process we can create a script that would allow the user to make their own training sets.  

How are your annotated genomes formatted? (ie how do you designate where the prophage regions are)

[Chris Brown]

Hi,
Thanks. I would format them as required. I am using published expert curated locations from reference genomes. I can convert the prophage location to gff3 or what was required, and use these in conjunction gff3 annotation for all genes from RefSeq or Prokka.
Cheers
Chris