PhAnToMe

Phage Annotation Tools and Methods

Prophages

Prophages are phages that have integrated into the bacterial genome. Some prophages get stuck inside the bacteria, and eventually get deleted by natural selection. Some prophages remain active - ready to pop back out of the genome and lyse their unsuspecting hosts.

For phage biologists, prophages have provided years of amusement. They are difficult, if not impossible, to classify, and although they often appear dead and decaying a simple recombination event (which happens all the time in phage world) is enough to bring them back to life - perhaps as a related phage, or perhaps as something completely different.

For microbiologists and microbial genomicists, prophages are something to be derided and ignored. "Those dead phage regions" are given no respect, and everyone thinks that they are just a pain.

For bioinformaticians, prophages are typically only found by looking for genes with homology. We find the things that we know about, and ignore the rest.

At PhAnToMe, we have taken a different approach. We have developed tools that will allow you to identify prophages even if they don't have any similarity to known phage genes. We have identified the prophages in the complete genomes, and we provide that data for you. We worry about prophages - are they still alive (where they ever??), will they come back to life, or are they destined for the evolutionary dead end, their DNA to be recycled into something not nearly so elegant.

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