Just a quick post to say how much I love PHAST, the PHAge Search Tool.
It looks for possible prophages in your bacterial genomes, and makes such beautiful pictures of the results, like this summary of the five phage it found in a new Salmonella genome:
And it will even show you a nicely annotated figure of indidual phage it found, using an interactive Flash viewer:
My only gripe is that unlike some of the more visualization-challenged phage finders, PHAST doesn’t output actual annotation files, like GenBank or GFF or even a simple text table that would be straightforward to convert into GenBank… the format in which it prints out the actual information on where each phage is located in your sequence seems to be a home-grown text format that is not easy to parse with existing tools.
Oh well, I suppose I will have to write a little script to turn PHAST’s phage hunt results into a proper annotation… unless someone else has already done this?