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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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Can we input virus(phage) sequences to identify the plasmid sequence in the virus sequence? #86

Closed Caiyulu-818 closed 3 months ago

Caiyulu-818 commented 3 months ago

Hi, can we input virus(phage) sequences to identify the plasmid sequence in the virus sequence?

From this result, can we assume that the recognized plasmid sequence is phage-plasmid?

apcamargo commented 3 months ago

Most phage-plasmids will be classified as virus by geNomad. What you can do is identify the sequences that have multiple PP, PV, or VP markers (you can read about these types of markers here). These markers are found in plasmids and can help you identifying phage-plasmids in a dataset.

Caiyulu-818 commented 3 months ago

Thank you very much for your reply! I will adopt your suggestion to find the specific plasmid markers~ ---- Replied Message ---- FromAntônio @.>Date04/02/2024 00:38 @.> @.>, @.>SubjectRe: [apcamargo/genomad] Can we input virus(phage) sequences to identify the plasmid sequence in the virus sequence? (Issue #86) Most phage-plasmids will be classified as virus by geNomad. What you can do is identify the sequences that have multiple PP, PV, or VP markers (you can read about these types of markers here). These markers are found in plasmids and can help you identifying phage-plasmids in a dataset. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

apcamargo commented 3 months ago

Let me know what you find!

Caiyulu-818 commented 3 months ago

Hi, @apcamargo Yes, I input the virus sequence, which I found in the plasmid summary file, some sequences were identified as plasmid with plasmid score >0.7( default mode),see attachment 1. Besides, I found there are multiply PP PV or PC markers in the plasmid gene summary (see attachment 2), whether these results can ensure these plasmids identified in the virus sequences are phage-plasmid? Best regards Lucy

apcamargo commented 3 months ago

Right now, there's no "standard" computational method to identify phage-plasmids. They are pretty much any element that share genes with both viruses and plasmids, so there's no rule of thumb. You can take a look at the distribution of PV/PP/VP markers in your data to evaluate a good cutoff.