Plasmid and Phage identification package

Question

[3335098459]

Hi,

I downloaded around 400 genomes from NCBI. I need to identify phages and plasmids if there is any. Is there any Linux based software that can identify plasmids/phages? Write those phages/plamsid sequences to a new separate file and the chromosomal sequences without plasmid/phages to other new files. My purpose is to analyze phylogeny with only chromosomal sequences. Guide me with your suggestions.

Thanks

[Fatima]

I think you can download prophage_virus.db from PHASTER and search against it.

https://phaster.ca/downloads/prophage_virus.db https://phaster.ca/databases

Answer 1

[Joe]

This isn't easy. There also isn't one tool that will do both.

There are loads of phage finder and plasmid detection tools online though, just googling those terms should yield lots of options.

Ones that come to mind:

Phages

• PHASTER
• PhiSpy
• ProphET
• Phigaro

(See a comparion by a guy I know here: https://nickp60.github.io/weird_one_offs/testing_3_prophage_finders/)

The names of several plasmid detectors escape me now, but I recall:

Plasmids

• PlasFlow
• PlasmidSeeker

Can't speak to the quality/usefulness of any of them myself though.

You might also be interested in AlienHunter which will look for IS elements etc.

Answer 2

[onestop_data]

I agree with Joe. For finding phages in bacterial genome, I know Phispy. I have written a step-by-step here on how to do it using FASTA to phage genomes.