Prokaryotic mobile element database

Question

[Lee Katz]

I was wondering what everyone's favorite database is to annotate mobile elements in prokaryotic genomes. I am using the Phast database which covers a lot of mobile genes, but unfortunately the main database I enjoy (IS Finder) is not something that I can download and so I am seeking an alternative.

Requirements: downloadable (local) database; IS elements; other mobile elements

[Lee Katz]

Bumping this back up to the top in case anyone has an actual IS element database.

[SES]

You could write a script to search sequences through the IS Finder web interface, or contact the authors of the site about downloading the database. They may be open to the second option, and it won't hurt to ask.

[Lee Katz]

I made that script a while ago, and they did NOT like that

Answer 1

[dago]

I like the program PHISPY for prophage discovery

Then for genomic island identification there is Islandviewer, that is quite nice.

[Lee Katz]

Thanks! What are the differences between PHISPY and PHAST? Islandviewer is really nice but I am not sure it is what I want since other genes might be on those Islands that are not mobile by themselves.

[dago]

I do not know PHAST so much, but as far I can read in the respective publications:

PHAST:

PHAST is not without some limitations. First, like all other database-driven annotation systems, PHAST obviously performs poorly at identifying novel phages, whose genes/proteins are not closely related to any record in the PHAST database. In this regard, the appearance of large numbers of proximal proteins with unknown function PHAST is not without some limitations. First, like all other database-driven annotation systems, PHAST obviously performs poorly at identifying novel phages, whose genes/proteins are not closely related to any record in the PHAST database. In this regard, the appearance of large numbers of proximal proteins with unknown function could be a good indication of a novel phage. could be a good indication of a novel phage.

PHISPY

PhiSpy was developed based on seven distinctive characteristics of prophages, i.e.protein length, transcription strand directionality,customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins

So it seems that PHSPY consider also contextual genomic features and the identificaiton it is not only DB driven.

[aadjiep]

How do you explain Phispy accuracy? I noticed it produced different results every run.