Link to this post | posted 10 May, 2022 13:59
mdgainey	Hi Rick, I am going to look into some of the these repeats with my students this summer. They also have a different repeat towards that middle of the genome where there are a lot of membrane proteins, and there are also a lot of gaps. You can also find them using MEME, and this generates a nice output to look at. I am going to give this another eyeball before I submit my final DJ annotation.

Link to this post | posted 28 Apr, 2022 17:21

mdgainey

I am working with a cluster DJ phage named Vardy this semester, that seems to have a surprising amount of membrane proteins (they called 16 initially), with many clustered together in the same area of the genome. There are also some with signal peptides in this area (predicted by signal P and topcons). I looked up the past signal peptide post and it seems that these we were not calling, but given that the idea here is just to alert someone about interesting areas of the genome where these membrane and potentially membrane associated proteins are, can I call these membrane proteins as well just to denote their presence for now, or can we add a signal peptide containing protein to the choices on the list? I will have some students look into this area a bit more this summer as it is also chocked full of interesting repeat sequences.

Link to this post | posted 09 Sep, 2021 17:34
mdgainey	I received a new computer this summer, and am currently trying to install the 2017VM. I thought I was good to go, but when I launch the VM I get an error: attempt to read or write outside of disk 'hdo' Does anyone know how to fix this?

Link to this post | posted 23 Jan, 2021 16:19
mdgainey	Thanks Debbie and Kirk,I missed this on the list due to not doing control F with the capital H in holliday. I felt like it should be there, and it is is….. Edited 23 Jan, 2021 16:19

Link to this post | posted 07 Jan, 2021 19:59

mdgainey

I am QCing the M3 bacteriophage Nanosmite, I ran into a similar issue and checked the request for new function list and it seems that this issue has not been resolved. The gene is Nanosmite_78 MARNRKSAKAAGARFEAQIAEALRNALGDPNIQRAPRWGAVDKGDIVNVRIDGHDLVIQTKDVTRLDLPKGVGDAKVQAVNAGALAGLFIHKRHGVGDPMKQWVSCTVAELVALITKVPVHPGAEEGIEGRAV All cluster members call holliday junction resolvase which is not on the official functions list, just Ruv-C-like or Ruv-A-like, and endonuclease VII. I am leaning toward just going with the flow and calling it a holliday junction resolvase, even though it it not on the official function list at this time, but would appreciate hearing other's opinions.

Link to this post | posted 10 Dec, 2020 18:14
mdgainey	Thanks Chris, they are going to test out some samples before we purchase one, and if I can get it to work well, I would be happy to share protocols.

Link to this post | posted 05 Dec, 2020 19:03
mdgainey	Hi all, has anyone used an SEM with a TEM detector to image their phages? We are hopefully going to be getting a new SEM with a TEM detector for our new science building next year, and I am hoping to use it to image our phages in house for the first time. We are still deciding on the specs to purchase, so any specific information would be helpful. Edited 05 Dec, 2020 19:04

Link to this post | posted 03 Jun, 2019 20:12
mdgainey	Okay, I think I will go with NKF.

Link to this post | posted 03 Jun, 2019 19:56
mdgainey	Thanks Debbie, I will rerun HHPRED, I was just going to call them assembly chaperones based on synteny.

Link to this post | posted 03 Jun, 2019 19:51

mdgainey

I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. I have not called a Major Capsid, but about half of other annotators call pham 10363 (FuzzBuster_31) a Major Capsid. I don't see any evidence for this and feel I should get nice HHPRED hits for a Major Capsid. I am not sure if this was called based on synteny alone, but perhaps I am missing something. I am leaning toward NKF.