Link to this post | posted 25 Mar, 2022 22:51

kcornely

Thank you, Steve and Debbie! We saw the pfam hit and it was one of the lines of evidence that convinced us that we should assign the function as a holin, but we didn't have convincing data that gp28 is a transmembrane protein. SOSUI classifies it as soluble, and TmmHm shows 0 predicted TMH. So thank you for letting us know that we should also be checking TOPCONS, which convincingly shows two transmembrane domains. In the future, we will check all three programs when we suspect a membrane protein. Thanks again!

Link to this post | posted 24 Mar, 2022 22:44

kcornely

Our team has a question on gp28 (pham 101034) of Langerak. We have a lot of evidence to assign its function as holin (synteny–follows lysins A and B, BLAST hits and HHPred hits), but according to the SEA PHAGES official function list, holins must have multiple transmembrane domains (which totally makes sense). But according to TmHmm and SOSUI, gp28 is soluble. Do we assign it as a holin? If we don't, is it all right to have lysin A and lysin B but not holin? We did notice that this protein is not assigned a function in closely related P1 cluster phages Donovan, Techage, Jebeks and HUHilltop. Thanks in advance for the help!

Link to this post | posted 17 Sep, 2021 19:39
kcornely	Hello all, I checked all of my preferences and they were exactly as Debbie's attachments showed, with the exception that I had checked "use active FTP protocol". When I unchecked the box, and then ran the auto-annotation after Debbie reported that GeneMark was back on line, it worked like a charm. Thanks for all of the help! Kathleen Edited 17 Sep, 2021 19:40

Link to this post | posted 15 Sep, 2021 23:52
kcornely	Thanks, Debbie! Unfortunately, I tried the auto-annotation again and it's still not working. I feel that maybe my Preferences aren't set correctly but I'm not sure what I'm doing wrong. Thanks for the offer of help; much appreciated! Kathleen

Link to this post | posted 15 Sep, 2021 19:29

kcornely

Greetings, all! I have a research student who is in the process of annotating a phage she discovered this past summer. When we did the auto-annotation, we got the genes called by Glimmer, but none called by GeneMark. We can get the GeneMark data from PECAAN, but it would be nice to have the GeneMark calls in DNA Master. We are running the most current version of DNA Master (5.23.6) and we set our Preferences to use the PBI server and we unchecked the boxes to the Glimmer and GeneMark servers. I am using a PC with Windows 10. I did have one question on the "Unlock Code" and "Password". The Word document shows an entry for the "Unlock Code" but "Password" is left blank. I tried it two ways (1) I entered the case-sensitive Unlock Code and left the Password blank and (2) I entered the same case-sensitive word in both the Unlock Code and Password. I got the same results both times–no GeneMark calls. As always, any help that anyone could provide would be much appreciated. Thanks, Kathleen

Link to this post | posted 21 Jun, 2021 22:33
kcornely	Chris, I hope that you had a nice visit with your sister. Thanks for the "whole page" Starterator report–I just downloaded it! I also had my student watch Kristin's video. Best wishes to you both, Kathleen

Link to this post | posted 21 Jun, 2021 17:21
kcornely	Kristin, we are accessing the reports through phagesdb, but I'd love to see your video! If we can't get the reports on phagesdb, we can go to PECAAN. I'm trying to wait as long as possible to introduce PECAAN because I want the new students to engage as much as possible with all of the other programs used in the annotation. Thanks!

Link to this post | posted 21 Jun, 2021 14:55

kcornely

Greetings, all, I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports? Thanks very much! Kathleen

Link to this post | posted 03 Jun, 2021 21:18

kcornely

Greetings, all! Thanks, Dan, your directions were super helpful. I noticed this recent post from Beckie in which she says that her copy of DNA Master is not "error-free". We are having some issues here as well. I have two new research students who installed DNA Master on their Macs in the emulator last week. I downloaded DNA Master on my new laptop (a PC), also last week. All three of us are having difficulties. I am having a problem updating DNA Master on my PC. I get an error message when I try to do so. My students are having similar update problems. Another problem that my students are having is that they are not able to BLAST individual genes (for example, when a different start choice is made). I've attached a screenshot so that you can see the error message my students are getting. Interestingly, there are no DNA Master difficulties on any computers on which DNA Master was installed sometime in the past. DNA Master works just fine on my home computer, my office computer, my lab computer and on the computers in the computer lab at the college. The problems we are having appear to be associated with recently-installed versions of DNA Master. Thanks in advance for any help you can provide! Kathleen 282Kb

Link to this post | posted 27 May, 2021 15:06

kcornely

Hi Debbie, Amazing how re-booting can solve so many problems! Yes, that worked. I'd also like to share the solution to another problem that this same student had when she first installed DNA Master in the Virtual Box. The DNA Master was in a very tiny window, and enlarging the size of the window just enlarged the white space. Here, in her own words, is how she solved the problem: "Open virtual box and click the “view” tab on the top right of the mac screen. Click “auto-resize guest display,” and expand/minimize the window size to whatever is desired, and the window should become full screen. Make sure to click anywhere inside the virtual box before going to the Mac drop down list so that the computer knows you want settings for virtual box." Thanks for the help! Kathleen