Link to this post | posted 20 Jan, 2019 00:31
welkin	Hi Nikki, So this is a very specific enzymatic activity. Can you differentiate between this, and say, just a generic amidase? HHPred can't always discern that level of specificity. IF you have good evidence for the specific activity, then sure. Otherwise, go with more generic.

Link to this post | posted 19 Jan, 2019 13:55
welkin	No. Band-7 proteins are their own class. Thanks for asking!

Link to this post | posted 14 Jan, 2019 20:08
welkin	I agree with Dan— It still looks like admin issues. I *think* you can move the entire already installed DNA Master folder from /Program Files to another location without reinstalling. Otherwise, make sure you set up the Desktop shortcut such that the program always launches with admin rights. Best, Welkin

Link to this post | posted 14 Jan, 2019 18:54
welkin	Hi Jackie, I think this still counts at MPME1. Best, Welkin

Link to this post | posted 14 Jan, 2019 18:53
welkin	Hi Manuel, that is definitely an out of date version. Current version on my computer is dated Nov 2019, and I just ran the updater and there is even a more recent one than that. Usually when the program refuses to update it is not being launched with admin rights. Best, Welkin

Link to this post | posted 14 Jan, 2019 16:48

welkin

One step growth curves in Mycobacteria are really hard. I've tried a number of times, but never really been satisfied with the data; it just doesn't look as nice as ones with E. coli or Salmonella phages. In general, we try for exponential cells with an OD of 0.4, and MOI of at least ten. We do the infection in a small volume (so you pellet your cells, resuspend in 1/10 or even smaller a volume); add phage; wait 15 min; and then bring back up to the initial volume. Shake at 37 for 3 hours or so while you sample. Latent periods seem to run around 3 hours-ish.

Link to this post | posted 10 Jan, 2019 13:14
welkin	yes, i agree— it stays a tail protein.

Link to this post | posted 08 Jan, 2019 19:23
welkin	Hi All, BAsed on this paper, https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22338 I think we are not going to add "FIC" to the list. As Dave said, FIC proteins are now identified just by a single short sequence, and can do all sorts of things. This means that we will not be adding this as a function at this time.

Link to this post | posted 08 Jan, 2019 14:22
welkin	Tell them not to open the program from the installer window, but to launch it the way we describe in the manual. They are probably launching with out admin rights if they go straight from install to open. Edited 08 Jan, 2019 14:23

Link to this post | posted 17 Dec, 2018 16:39
welkin	Hi Julia, The annotating school absolutely gets author credit in GenBank. I like the idea of adding an "annotated by" box to phagesdb…. I will look into making it happen.