Link to this post | posted 16 Apr, 2019 18:43
debbie	i haven't found it either.

Link to this post | posted 16 Apr, 2019 15:17
debbie	We can ask Claire about the glitch. Yes, you can still transfer data from PECAAN into DNA Master for your final file. debbie

Link to this post | posted 13 Apr, 2019 18:58

debbie

Sally, I asked Graham, and he agrees we can call these RexA and RexB. I think that RexA and RexB are a sufficient name. I would not include toxin/antitoxin because it is a known abortive infection mechanism. Toxin/antitoxin is too broad and we know the specifics. For the official list, would you confirm that gene 41 is the RexA and gene 43 is the RexB? (or what genes they are when you re-number?) Cool! debbie

Link to this post | posted 13 Apr, 2019 01:26
debbie	Jackie, It is annotated as a gene with 2 regions (just like a programmed frameshift). GenBank will squawk about it, phamerator won't like it, but that is how you will submit the file. Biologically, the phage doesn't care, it exists in the host as a circle.

Link to this post | posted 11 Apr, 2019 18:43
debbie	Greg, Again I haven't looked, a 28% hit to terminase could be a DNA binding domain, an ATPase domain, or a nuclease domain hit. This may not even be related to a terminase. Let me know if you really need me to look.

Link to this post | posted 11 Apr, 2019 17:52
debbie	Greg, Without looking, could your terminase,large subunits be hitting different parts of terminase? so you have a modular configuration of as in Auxillium gp2 and gp3, with one gene matching ATPase domain and the other matching a nuclease domain? debbie

Link to this post | posted 11 Apr, 2019 17:42

debbie

Hi Deb, As I look at this more closely (I HHPred'd BeeBee8 and Velene), the hits are alignments to their N-terminals (the last 20-25 amino acids). The predominant hit is to zinc-finger domains. I think that is what our protein is hitting - a zinc finger domain. Without more information, we should label these as Hypothetical Proteins. FYI - the rationale to DNA binding domains is that I think the zinc fingers were a term coined to mean a structure that inevitably binds to DNA (or RNA) using zinc ions. I think Wikipedia does a nice job of describing the specific and general use of the term 'zinc finger' and why we have not adopted it (since it now holds such a generalized meaning). https://en.wikipedia.org/wiki/Zinc_finger Edited 11 Apr, 2019 18:50

Link to this post | posted 08 Apr, 2019 17:05
debbie	Nice!

Link to this post | posted 05 Apr, 2019 17:58
debbie	Friday at 2pm. Seems to be working fine. Were you adding a phage? I did not try that, but I could review phages.

Link to this post | posted 03 Apr, 2019 02:23
debbie	Hi! Wow! More details are needed. Would you provide who you are, Where you are from, What host you are using? Once I get some basics, I may have more questions.