SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

All posts created by welkin

| 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.

Best,
Welkin
Posted in: DNA MasterImportant DNA Master Update
| posted 16 Jan, 2018 15:42
Hello,
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:

http://www.techrepublic.com/blog/windows-and-office/selectively-disable-uac-for-your-trusted-vista-applications/​

Cheers,
Nan"


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
Done!
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
| posted 08 Nov, 2017 18:15
Hi Beckie,
IT sounds like there is a problem with at least one of the internal tables in the file.
If you have the documentation, I would try to regenerate a clean copy of the file by importing the fasta sequence into a new file, pasting in the documentation, and then parsing that.

Good luck.
Posted in: DNA MasterTbRegions: Cannot perform this operation on a closed dataset
| posted 03 Nov, 2017 16:57
Hi All,
Here are the instructions for posting this this forum.
First: check the most recent Official Functions list. This list has moved online!

Next, if you want to continue with your request:
1. Start a new thread. Don't tack your request onto to the end of an old thread.
2. Present your case by answering the following questions.
What is your evidence that your phage protein has the putative new function? Include alignment tool, database used, phage name/gene number, or other evidence.
How large are known proteins of this type? Is the size of the protein you are investigating of similar size?
Are there conserved residues that are characteristic of this domain? Does your protein have them?
Are there normally other conserved domain present in conjunction with this domain? Does your protein have them?
3. please include links to primary literature (preferred!) or database entries that support your claims.
4. Post the amino acid sequence of the gene in question, so we can copy/paste for further analysis if need be.
5. Upload your most current DNA Master file as an attachment to your post.

Finally—In general, we don't like to put structural domains down as functional assignments, as too many proteins with a variety of functions can include them. This includes "alpha helix", "beta strand" "coiled coil" "zinc-finger" "von Willebrand factor" etc.

Happy functions!

Welkin
Edited 08 Nov, 2017 15:25
Posted in: Request a new function on the SEA-PHAGES official listREAD THIS BEFORE YOU POST