Link to this post | posted 16 Jun, 2021 21:26

debbie

Simon White’s cryo EMs of mycobacteriophage Rosebush show that the MuF-like minor capsid is NOT part of the capsid. (SO do not call it.) He did find 2 different capsid proteins in RoseBush, one that makes the hexamer (gp 15) and one that makes the pentamer (gp16). These two capsid proteins are in all of the Cluster B genomes. See the SEA-PHAGES Functional Assignment Sheet for correct naming. Edited 06 Apr, 2022 17:42

Link to this post | posted 09 Jun, 2021 15:49
debbie	Steve, I think that Pitt servers were down for a bit this am. Here is the install download. https://www.dropbox.com/sh/ygbayg8zqy32wiq/AADM8F9-RXkkSYXVFA-hhhPza?dl=0

Link to this post | posted 03 Jun, 2021 23:49

debbie

I am adding a response from Chris Shaffer: I did a bit on this. Mostly on the question of nomenclature, not on the validity of the specific gene call. Because of this investigation, I am removing the DnaC-like helicase loader from the approved list. I also ran across this site in poking around the web which is kinda interesting site: https://proteopedia.org/wiki/index.php/DnaC_helicase_loader It says there are two types of helicase loaders: DnaC helicase loader (DnaC) transfers helicase to replication origins. The helicase loaders belong to two classes. The ‘ring breakers’ break the hexameric helicase to allow the DNA to pass through. The ‘ring makers’ assemble the helicase monomers to hexamers around the DNA. Here is a good paper that summarizes these two methods: https://pubmed.ncbi.nlm.nih.gov/12906810/ Unfortunately, there is a complication in that the E coli DnaC is a breaker type and the B subtilis DnaC is a maker type so we have a name crash. This is the kind of thing that makes it really easy to make mis-assignments and/or cause a lot of confusion. If we say "DnaC-like" do we mean the E coli or B sublitis version. So I would argue for this situation, the best solution is to update the terms list to just "helicase loader" and avoid the "DnaC like". I will note in my BLAST searches I found two Bacillus phage proteins that Veronique has published using the term "helicase loader" so she agrees with me.

Link to this post | posted 03 Jun, 2021 23:14
debbie	You are welcome!

Link to this post | posted 03 Jun, 2021 21:35

debbie

Hi Kathleen, I am no expert, but the error is because DNA Master was written before the era of secure https. I believe that you are missing some SSL libraries. I had referred to these in the past, but I am not confident that they work. https://www.dropbox.com/sh/mtvey9ohuuykv7r/AADuZje-yHWf1SIRDE0eg9gVa?dl=0 His issue was then, where to put them. They are located in the main DNA Master folder on my computers (in Program files), so put them there. But, if that doesn't work or you like his advice better, here is another option. Christian Gauthier found the right stuff that worked for him here. For your future reference on this point, a lightweight program that folks can install to fix this issue is the Bitvise SSH Client (https://www.bitvise.com/ssh-client-download). Apparently it puts everything in the right place because DNA Master is now performing remote BLAST jobs without complaint! Fingers crossed! debbie Edited 03 Jun, 2021 21:36

Link to this post | posted 01 Jun, 2021 10:32
debbie	Hi Kari, Short and repetitive sequences are the culprits; some of the default settings for QBlast are probably different might exclude too much. That would lead to a very high EValue threshold, so no Results. Very little in QBLAST is specified by the user. In order words, it is an internal DNA Master setting. Just note that DNA Master wouldn't Blast it on your cover sheet. Thanks, debbie

Link to this post | posted 27 May, 2021 15:20
debbie	Terrific! Thank you!

Link to this post | posted 27 May, 2021 00:18
debbie	Hi Joe, Sorry, that is my fault. I didn't mean to make it confusing. I was thinking about the minimal file and you are talking about the complete notes file. The rationale for using is the function field is so that the product field can be deleted and then re-populated from the function field. I hope that makes sense. debbie

Link to this post | posted 27 May, 2021 00:16
debbie	Becky, I asked around because I don't use Wine. Tammy Adair (at Baylor) offered this: "As far as I can tell we cannot use wine on any systems past Catalina . Most of my Mac students used a virtual machine set up that our IT department provided. The IT guy that I have been working with for the past 10 years does not see a fix.".

Link to this post | posted 26 May, 2021 22:31
debbie	Hi Kathleen, Did you shutdown the computer and restart? debbie