SEA-PHAGES | All posts created by hnance@ccga.edu

Link to this post \| posted 27 Mar, 2025 15:27
hnance@ccga.edu	kbutela hnance@ccga.edu Hi all, Anyone having a hard time getting DNA Master to update? This isn't for a new installation, just a regular update and shut down. On multiple computers on campus, the program won't update and either shuts down while trying to update or must be shut down using Task Manager in Windows. The program seems to work fine, otherwise. Thanks! Holly The DNA Master update server is currently down as of 3/27/2025. As long as you have version 5.23.6, build 2705, 24 October 2021, you do NOT need to update DNA Master. I'd recommend turning off automatic updates by navigating to Preferences –> Timed Events and unchecking the "Automatic checks for DNA Master updates" box. Thanks for the prompt reply!

Link to this post | posted 27 Mar, 2025 15:27

kbutela
hnance@ccga.edu
Hi all,
Anyone having a hard time getting DNA Master to update? This isn't for a new installation, just a regular update and shut down. On multiple computers on campus, the program won't update and either shuts down while trying to update or must be shut down using Task Manager in Windows. The program seems to work fine, otherwise.
Thanks!
Holly

The DNA Master update server is currently down as of 3/27/2025. As long as you have version 5.23.6, build 2705, 24 October 2021, you do NOT need to update DNA Master. I'd recommend turning off automatic updates by navigating to Preferences –> Timed Events and unchecking the "Automatic checks for DNA Master updates" box.

Thanks for the prompt reply!

Posted in: Bioinformatic Tools and Analyses → DNA Master not updating

Link to this post \| posted 27 Mar, 2025 15:11
hnance@ccga.edu	Hi all, Anyone having a hard time getting DNA Master to update? This isn't for a new installation, just a regular update and shut down. On multiple computers on campus, the program won't update and either shuts down while trying to update or must be shut down using Task Manager in Windows. The program seems to work fine, otherwise. Thanks! Holly

Posted in: Bioinformatic Tools and Analyses → DNA Master not updating

Link to this post \| posted 06 Feb, 2025 18:06
hnance@ccga.edu	debbie Hi Holly, I recommend that you follow Sally's advice and call it an "ASCE ATPase". Thanks! debbie Got it - thank you! Holly

Posted in: Cluster EA Annotation Tips → AAA ATPase or RecA recombinase?

Link to this post \| posted 06 Feb, 2025 17:39
hnance@ccga.edu	Gene 35 (stop 23126) in LilTerminator is called AAA ATPase in most phage in the PhagesDB database. However, the Function List says not to call this anymore. Based on Sally Malloy's ppt on when to call it RecA-like recombinase and when to call it ASCE ATPase, I don't think LilTerminator 35 has all features to call it RecA. But cluster EA is not listed under those clusters that don't have RecA recombinase, but do align to a core ATPase. Any advice on what to call this gene? Thank you!

Link to this post | posted 06 Feb, 2025 17:39

hnance@ccga.edu

Gene 35 (stop 23126) in LilTerminator is called AAA ATPase in most phage in the PhagesDB database. However, the Function List says not to call this anymore. Based on Sally Malloy's ppt on when to call it RecA-like recombinase and when to call it ASCE ATPase, I don't think LilTerminator 35 has all features to call it RecA. But cluster EA is not listed under those clusters that don't have RecA recombinase, but do align to a core ATPase. Any advice on what to call this gene? Thank you!

Posted in: Cluster EA Annotation Tips → AAA ATPase or RecA recombinase?

Link to this post \| posted 31 Jan, 2024 10:54
hnance@ccga.edu	Thanks for clarifying this. So we only need one domain identified by TMHMM to call a membrane protein? Thanks again! Holly

Posted in: Annotation → Membrane proteins

Link to this post \| posted 30 Jan, 2024 16:57
hnance@ccga.edu	I'm having trouble finding another program besides TMHMM to run online to predict membrane proteins. I've got evidence of one domain with TMHMM, but it sounds like I need another prediction program to call this a membrane protein. I can't find how to access SOSUI online. Thanks! Holly

Posted in: Annotation → Membrane proteins

Link to this post \| posted 29 Jan, 2024 10:42
hnance@ccga.edu	Thanks for looking into this! I will share the attached paper with my students as a great reminder for why we annotate. Thanks again! Holly

Posted in: Phamerator → Missing gene in PhagesDB draft genome

Link to this post \| posted 26 Jan, 2024 20:41
hnance@ccga.edu	Hi Debbie, Thanks for the prompt reply. I understand that numbers won't match, and the stop is how they ought to be identified. But I'd never seen a gene number skipped in Phamerator. However, it sounds like it's not a big deal, so I will move ahead! Thanks again for your help!! Holly

Posted in: Phamerator → Missing gene in PhagesDB draft genome

Link to this post \| posted 26 Jan, 2024 19:38
hnance@ccga.edu	Hi, It looks like Poultress is missing Gene 33 in the PhagesDB database. The draft genome in PhagesDB counts Gene 32 and the next is 34. Gene 34 in PhagesDB corresponds to the coordinates I have for Gene 33 (start 22659, stop 22994) in my autoannotation file. Is there a reason the database would skip a gene number? This skipped gene number (Gene 33) is missing in Phamerator, too. Thoughts? Thanks!!

Link to this post | posted 26 Jan, 2024 19:38

hnance@ccga.edu

Hi, It looks like Poultress is missing Gene 33 in the PhagesDB database. The draft genome in PhagesDB counts Gene 32 and the next is 34. Gene 34 in PhagesDB corresponds to the coordinates I have for Gene 33 (start 22659, stop 22994) in my autoannotation file. Is there a reason the database would skip a gene number? This skipped gene number (Gene 33) is missing in Phamerator, too. Thoughts? Thanks!!

Posted in: Phamerator → Missing gene in PhagesDB draft genome

Link to this post \| posted 20 Jan, 2023 11:52
hnance@ccga.edu	Hi Debbie, Thanks for your prompt reply! Mopey_14 doesn't hit D29_16 in HHPred or BLAST, but it hits the same protein that D29_16 hits if you run D29_16 in HHPred (both Mopey_14 and D29_16 hit 6BOXG, which is a scaffolding protein). After asking my question yesterday, I had convinced myself that it was a silly question because Mopey_14 and D29_16 are not in the same phamilies. But it sounds like despite that, the structural homology warrants both being scaffolding proteins. So far, Mopey has several genes for which the function call is tricky as there is not consensus in the cluster. The timing of your meeting last Friday was great! Thanks again so much for your help - Holly

Link to this post | posted 20 Jan, 2023 11:52

hnance@ccga.edu

Hi Debbie,

Thanks for your prompt reply! Mopey_14 doesn't hit D29_16 in HHPred or BLAST, but it hits the same protein that D29_16 hits if you run D29_16 in HHPred (both Mopey_14 and D29_16 hit 6BOXG, which is a scaffolding protein).

After asking my question yesterday, I had convinced myself that it was a silly question because Mopey_14 and D29_16 are not in the same phamilies. But it sounds like despite that, the structural homology warrants both being scaffolding proteins.

So far, Mopey has several genes for which the function call is tricky as there is not consensus in the cluster. The timing of your meeting last Friday was great!

Thanks again so much for your help - Holly

Posted in: Functional Annotation → Scaffolding protein

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