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padlocbio / padloc

Locate antiviral defence systems in prokaryotic genomes
MIT License
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Solitary genes #22

Closed Liqueurdefehling closed 1 year ago

Liqueurdefehling commented 2 years ago

Hi,

Does an option exist to show not only complete systems, but also solitary genes such as solitary methyltransferases ? In other words, can we have access to the full landscape of defense genes, even if they are not included in complete systems?

Best, Auriane

leightonpayne commented 1 year ago

No option exists currently, other than inspecting the raw output of HMMER (*.domtblout), although this will give you all the hits pre-e-value filtering. We could add a feature for returning all solitary genes, but our e-value cutoffs have not been optimised for this purpose - and the results would likely require further post-filtering.

I'll re-open this issue if this ever get added.