In silico prediction if a phage can invade a bacterium
2
1
Entering edit mode
4 weeks ago
A_heath ▴ 170

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 • 419 views
ADD COMMENT
4
Entering edit mode
4 weeks ago

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.

ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
2
Entering edit mode

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.

ADD REPLY
2
Entering edit mode
4 weeks ago
Mensur Dlakic ★ 29k

This paper predicts virus-host associations:

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

ADD COMMENT
1
Entering edit mode

Many thanks for your suggestion,

ADD REPLY

Login before adding your answer.

Traffic: 1535 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6