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

Link to this post | posted 21 Jan, 2022 18:06
debbie	Yes. That matches the page I attached above. But don't get confused. It is not what appears in the Glimmer and GeneMark fields that is important. They could actually be empty. What is important is that the check box is checked and the the unlock code is entered.

Link to this post | posted 20 Jan, 2022 21:51
debbie	Chris, We run Glimmer and Genemark on Pitt servers, so the update from 2017 is no longer applicable. debbie

Link to this post | posted 20 Jan, 2022 19:29
debbie	Chris, I am not sure what you are answering but do your DNA master preference panes look like this? Edited 20 Jan, 2022 19:40 637Kb

Link to this post | posted 19 Jan, 2022 01:22
debbie	Chris, I am guessing that you do not have all of the preferences set correctly. In particular, make sure that #2 and 6 are correct. Let me know, debbie

Link to this post | posted 14 Jan, 2022 22:44

debbie

Hi Kyle, The simple answer to you questions and assumptions is yes! The SMART Team is pretty smart and I think they will be able to follow whatever you provide. The purpose of these notes is 2-fold. One is help get to best answer in the genome review process. If you get to the best answer, they don't have to spend a lot of time in your notes. But, if they find the annotation lacking, the documentation of how you made the calls can help them. The second is to help you - the annotator - document your gene calls so that we can help where needed. We can't help you and you can't help you if you can't see the rationale of what you did. Don't over think this, make your notes meaningful and it will all work out. Check out the links posted above for more of the rationale. Sounds scary, but should simply. debbie