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All posts created by welkin

| posted 09 Feb, 2018 19:22
so i am trying to remember why we picked the sequence we did: i think it had some thing to with stop codons or a lack of conserved sequences across the cluster. our initial choice in phage 1 was proven wrong when examined in the context of phages 2, 3, 4 etc; and the weird sequence was the only choice left.
i would have to dig through my notes to recreate it.

Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 23 Jan, 2018 20:49
I am having a hard time following all this. If you have a brand new machine that DNA MAster has never been on, and you download the installer from JEffrey's website, it will be an old version. He does not update the version of the stable installer very often. This is because a bunch of drivers, etc, come packed with it. It is much easier on his end to leave the installer alone, and then ask everyone to immediately update to the newest version once you install it.

So: Once the program is installed, everyone should immediately run the DNA Master update function to update to the newest version.
Sometimes JEffrey's server does go down, and when this happens no one will be able to update. you should write to us if you can't connect to the server so we can investigate.

Please note: sometimes students get confused between the installer file and the executable file. They keep launching the installer and wondering why the program never opens.
The executable that launches the program is called DNAMas.exe and will be found
C:\\Program files(x86)\DNA Master\DNAMas.exe

Do not move that executable out of its directory, or it will not be able to find its helper files, and will not launch correctly.

I think I covered everything— let me know if there are still
Posted in: DNA MasterProblem installing DNA Master on Windows 10
| posted 23 Jan, 2018 20:37
Hi Cuong,
You will need some way to access Windows for DNA Master. the "SEA Virtual Machine" specifically refers to a frozen Ubuntu image that contains Phamerater and STarteror pre-installed.

Posted in: DNA MasterImportant DNA Master Update
| posted 16 Jan, 2018 15:42
A number of you have asked about DNA Master and Windows 10. The program runs fine on Windows 10. If you are having difficulty with regular users running the program with admin privileges in computer labs, please show the following to your IT person to set up the computers. It was written by a Pitt IT specialist who set up our computer cluster with DNA Master on Windows 10 machines.

"So as I mentioned, the problem was that as a regular user - windows had an issue with the software being from an "untrusted" developer.

I used the Application Compatibility Toolkit to manually add the title to the windows whitelist for such things. After that, no problem running as a regular user.

I used this guide to resolve the problem, substituting the windows 8.1 versions where appropriate:​


Posted in: DNA MasterDNA Master and Windows 10
| posted 02 Jan, 2018 13:45
I am happy to add "lysin A, [insert domain name here]" to the list if you have some specific suggestions?
Posted in: Functional AnnotationLysins in Gordonia
| posted 30 Dec, 2017 11:20
sounds good!

I added amidoligase and glutamine amidotransferase domain to the list, as that is what you called them in the post. Do you think it should be amidotransferase domain and carboxylate amine ligase, as you wrote in the title of the post? which is the most accurate without being overly specific?
Edited 30 Dec, 2017 11:24
Posted in: Request a new function on the SEA-PHAGES official listamidotransferase domain and carboxylate amine ligase
| posted 30 Dec, 2017 11:19
Hi Jordan,
So what exactly are you proposing?
86 is BrnT rather than RelE, and and 87 is RelB? Does BrnT have its own anti-toxin we should be looking for?
Posted in: Request a new function on the SEA-PHAGES official listRibonuclease toxin BrnT
| posted 20 Dec, 2017 15:42
Posted in: Cluster B Annotation TipsGTP cyclohydrolase I
| posted 18 Dec, 2017 16:51
Cool! Sarah, check to see if it is split into two functional domains like in some of the Gordonia phages. This would be the first example of this in the Mycobacteriophages.
Posted in: Gene or not a GeneLysin A split in 2 or sequencing error-B1 cluster
| posted 18 Dec, 2017 16:50
Thanks Chris.
I think we will have to meditate on this one a bit and get back to you.
Posted in: Request a new function on the SEA-PHAGES official listThird type of Holiday junction resolvase