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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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lifestyle prediction #58

Closed ucassee closed 2 years ago

ucassee commented 2 years ago

Hello,

I was wondering how VIBRANT predicts the lifestyle of viruses? What is the training data (marker proteins or whatever) you used to predict lifestyle? I don't find the detailed information in your paper, maybe I missed that.

Thanks

KrisKieft commented 2 years ago

Here's a quick summary. Let me know if you want any more details about it.

Prophage: see details in the manuscript on how prophages are excised. Basically, v-scores are used to cut at bacteria-like (low v-score) regions and then the excised sequence is run through the pipeline to see if it's a virus. Excised prophages are lysogenic.

Lysogenic: any virus that encodes an integrase-like annotation and all prophages.

Lytic: any virus not excised as a prophage and not identified as lysogenic (no integrase-like annotation). This category will be slightly over-estimated since any true lysogenic phage that is only a partial sequence without an integrase will be mis-identified as lytic.

ucassee commented 2 years ago

The summary is fine for me. Thanks for your quick reply!