Hi,

Sorry for not having answered earlier. For a reason I don't understand I had lost connection with my ResearchGate account and hence did not see your message

I have a quite straightforward approach to search for transposable prophages : I use a set of 10 well conserved proteins, GemA, Mor, portal and the transposition proteins TnpA and TnpB from both phage Mu and B3. I take the genomes that have the one copy of at least one set on a 35-39 kB region. I extract the sequences, usually repredict genes with GeneMark to have something homogenous, and blast the proteins sequences vs ACLAME virus and prophage proteins (http://aclame.ulb.ac.be/Tools/blast.html, choose "viruses and prophages" in the box up right). That gives me the list of existing ACLAME protein families represented on each of my putative prophage, so that I can easily recognize the other most conserved proteins present and the other proteins expected to be found on a prophage. I'm actually writing that down right now for a paper on a series of B3-like prophages I've identified in Enterobacteria and Spirochetes. I'll send that to you as soon as it's ready (in a few days I hope) so that you can tell me if it is sufficiently detailed to be useful as a procedure. I do a lot of this by hand but I'm sure an algorithm could be written to do that at least partially automatic. Prophinder and other predicting programs don't perform too well for this type of phages because they often have a large non conserved region which lowers the score, such that one arm is often removed from the prediction. I also think that a fraction of these prophages raise problems at the level of sequence assembly because if they are present in more than one copy (which has no reason not to happen) the prophage borders are difficult to assemble and hence the prophage appears on a single contig, which is missing the prophage ends. Another problem more specific to enteric transposable prophages is that they sometimes carry an invertible region, which also messes up assembly such that the prophages comes up in three pieces...

Hope this helps. Regards. Ariane.

Thanks a lot for your reply. I am sure that your comment can help me to understand more about prophages and their properties. I will be in touch with your work and will contact you whenever I come across a problem or find something interesting.

During my insilico work with different phages and their hypothetical proteins! I came across various novel functions associated with them. I think hypothetical proteins holds a key in attributing new characters through horizontal gene transfer to their bacterial hosts. Many are associated with resistance, pathogenicity as well as metabolism associated genes totally unrelated to phages. Considering non-Specificity associated with phages as reported by many researchers; it seems that this transfer plays a major role!

Let's see what we come up in the future.

Thanks once again!