Link to this post | posted 15 Feb, 2022 17:44
debbie	Hi Fred, I don't know enough about DNABIND or DNA Binder to know how good that they are predicting DNA binding proteins. An analysis of what we have called DNA binding proteins with these programs is in order to determine if we would want to adopt this, I think. Make sense? debbie

Link to this post | posted 15 Feb, 2022 16:27
debbie	Hi! You should have bacterial growth! But if it is a lysogen, that bacterial growth should be releasing phage, so around the bacteria streak you will see a zone of lysis. You can see a tiny zone of lysis around A and D. But it is not easy to tell. What phage are you working with? debbie

Link to this post | posted 15 Feb, 2022 13:38

debbie

Adam, At the crux of the membrane protein designation is "what constitutes a membrane protein?". We have established a rule. (Know that phages don't have rules, so this is problematic.) The rule is if a protein has 2 or more transmembrane domains, call it a membrane protein. However, if it only has one, you must confirm the transmembrane domain with another transmembrane finder. Most recommended finders are TMHMM and SOSUI. PECAAN is using TopCons, which might be more helpful if we could agree on how to interpret it. However, Phamerator does not remove anything protein labels, ever. What can happen is that at Pitt, I have a team who are curating the functional calls (discrepancies) by phams. Our 'corrections' go directly to the GenBank file. Phamerator systematically checks changes in GenBank files and updates. You are right, membrane protein is not a functional call. It can be informative. Unfortunately, over time we have waffled on the one transmembrane call so those calls may or may not be there.

Link to this post | posted 11 Feb, 2022 22:40
debbie	Welcome!

Link to this post | posted 11 Feb, 2022 18:48

debbie

Hi all, If what you are worried about is the the overlappedness (I just made that word up, I think) between the C terminus of the forward facing gene and the C terminus of the reverse facing gene, I would suggest that that will have no bearing on whether these two genes get expressed. Where this does matter is at the N terminus, and its possible DNA binding sequences/promoters and such. We try to make sure there is room for the 'stuff' that genes need to get transcribed and translated. We have many examples of this in the database. debbie

Link to this post | posted 11 Feb, 2022 18:42
debbie	I think that the answer is more complicated than that. Can we set up a time to chat about this? The distinction may be arbitrary, but more information is needed and starterator - by itself- will not have all of the answers. I am happy to review this with you and your students! debbie

Link to this post | posted 10 Feb, 2022 03:48
debbie	We'll need to do some further investigations, I think. Without experimental data, I am bit uncomfortable to call this more specifically than an "RNA binding protein". I have attached an article that describes 3 different RNA binding protein families. How would one differentiate between them? Knowing that would help in this decision. Still thinking. debbie 864Kb

Link to this post | posted 10 Feb, 2022 03:30

debbie

Rick, When I look at the data I see gene 25 (19067 - 19582) has a pFam hit to TAC. I see that gene 24 (18604 - 19014) has 3 pFam hits - one to a capsid, one to a tail, and one to HK97gp10 (that we don't know where it is in the structure - a head or tail?) So that is just confusing. I am sure that we overcalled the slippage in CloverMinnie (because at that moment in time, we thought there had to be a slippage (and now we don't)). So I would not use that one for reference. Likewise I think gene 23 (18266 - 18607)is a Hypothetical Protein. debbie

Link to this post | posted 08 Feb, 2022 16:10

debbie

Hi Amaya, We had this problem this summer. This fails because DNA master is set to an active FTP stie, and it has to be changed to passive. But until you get an update, you don't have that option. Kristen Butela was able to work through it, so try this. Be sure to be running as administrator as you update. From Kristen: I figured it out! For a fresh install, you need to first update DNA Master from the help menu. This appears to go through successfully, and I got the message about the update being finished after restarting the program. I then restarted the program, and this is where I was getting the error messages and eventual FTP failure when retrieving helper programs. However, I just ignored all of those messages and clicked to make them go away. After the "Retrieving Helper Programs" update finally stalled at the 3% mark and threw the ftp error message, I went back to Preferences. The Home Site button is now there, so that initial update round must have updated the Preferences panel. I just unchecked the Active FTP connection box and applied changes. I then re-updated DNA Master, and everything went through with no error messages. This is an easy work around that only takes a few extra seconds. I'm happy to make a video and post it to the forums if that would be helpful. Kristen

Link to this post | posted 04 Feb, 2022 20:21

debbie

I think I corrected the confusion on the approved function list. Note that 'protein' was never mentioned in the first column. The biology confusion is that "is a 'helix-turn-helix' a protein function?". That is the original of the use of domain. We are saying that this protein has a helix-turn-helix domain in it, but what it does (other than fit into DNA nicely), is varied. Does this help? debbie Edited 15 Feb, 2022 13:23