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In silico prediction if a phage can invade a bacterium

Dear all,

I have the .fasta sequences of a phage and a bacterial strain. I would like to know if this phage can invade the bacterium I am studying. What type of tools could you advise me to use for this, please?

I thought about PHISDetector but it has a large database (>100 Gb) ..

Many thanks for your help!

phage bacterium
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written by A_heath • A_heath

2 answers

Most phage-host prediction tools determine a phage's potential host by analyzing similarities between the phage and bacterial genomes. These similarities may include shared genes, prophages, CRISPR spacers, tRNA, and other genetic markers. The underlying assumption is that the bacterial genome most similar to the query phage genome is likely its host.

To predict the host of your phage, you can compare its genome against a database of bacterial genomes to identify potential matches. Additionally, you can use NCBI BLAST to check if your phage is similar to other phages with known hosts, which may provide further insights.

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written by Andrzej Zielezinski Andrzej Zielezinski

Thank you for your kind reply, I want to analyze specifically the bacterium I have the fasta file of. Indeed, PB-LKS provided a predicted probability that the bacteria is the host of the phage, but I would like to know if other tools could help me to know is there is a risk of invasion.

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written by A_heath • A_heath

BLAST your query phage genome against genomes of bacteria (e.g., I would recommend the GTDB database) and check which other bacterial strains or species appear in the results besides your bacterial strain of interest.

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written by Andrzej Zielezinski Andrzej Zielezinski

This paper predicts virus-host associations:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012597

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written by Mensur Dlakic Mensur Dlakic

Many thanks for your suggestion,

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written by A_heath • A_heath

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