Lee Hughes
Dan - I have a student who wants to install the VM on his computer. Can I get the link please?

Thanks,
Lee

cmageeney
QUESTIONS:

1. Are both blasts really necessary?
Both blast are important because they give you different data. The NCBI blast will give you all information while phagesdb blast will only give you actinobacter phages. You can however individually blast each gene product as you annotate in DNAmaster. I find this helpful for students since they can then make start site changes and re-blast, when necessary. What I typically do is set my personal file to blast overnight. I have never had a problem doing it that way then I have all the data needed.

2. What might the PhagesDB BLASTp turn up that the NCBI would not (archived phage genes, I suppose.)?
phagedb is going to show all the blast hits in actinobacter phages. This may be useful if you are looking for other phages that are not in genbank yet.

3. What might the NCBI BLASTp turn up that the PhagesDB BLASTp would not? So far, they are identical.
NCBI will turn up many additional results that phagesdb is not set for. These could be hits in bacterial species, other types of phages, such as coli phages.

4. HHPred returns completely different regional homologies. Is there a threshold, i.e. number of AAs in a string that might be of interest?
We ask our students to use their best judgement about functional information here. I use 95% homology and e-values higher than 10^-5. This is not a hard rule but a good guideline to start with.

5. In HHPred if the query sequence is 150aa long and a homologous stretch of 18-20aa is return in say an "E. coli DNA Gyrase Inhibitor" can/should we ignore such short homologies?
Take all information into consideration but use your best judgement.

Hope this helps and anyone else that has information to answer these that I might have missed feel free to jump in.

Lee Hughes
I just ignore the updates personally. I might change to the new version after a semester, but never during. Don't want to take any chances that things will get mucked up.

ksaville
yep - it showed up now. I found Timmi and he wasn't trapped in a well.

Thanks

Kristen Butela
Hi there Greg! Yes, I am currently still using WINE to run DNA Master. The great thing about WINE is that it really isn't a Windows emulator that requires a separate virtual machine-any WINE program can run on the native MacOS. From my understanding, WINE in combination with X11 provides a basic scaffold on the Mac on which Windows programs can run. All you need to do is to make sure that XQuartz/X11 (http://www.xquartz.org/) is installed on the computer (this permits WINE programs to function). Tamarah's link contains the entire DNA Master package. The Mac will treat this program as an app. Good luck, and let me know if you have any questions!

GregFrederick@letu.edu

Tamarah Adair
We are running DNA Master within the WINE configuration.
The installer has been copied and you should be able to get to it from this link.
https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz

Our contact is in Student Technology Services. He installs the DNA Master on the Macs in the lab at the beginning of the spring semester. If there are updates he incorporates these. I'm sure he would be glad to answer any questions you might have.

Hey Tammy. I'm not a Mac guy… I used one some 20 years ago… but it has been a while.

Your link above still works. It leads to file called DNAMaster_5.22.19.dmg

Is that an executable file on Mac OS10? Does it need to be extracted? Or opened in another program? Sorry for the newb questions!

Thanks! Greg

klloyd-davies
Hi Dan,

I work at WSU's VetMed IT and have been asked to install the VM in one of our student labs per Bill Davis. He provided the software and I've got it up and running, but I need admin credentials to install the Guest Additions. Would you be able to email me the password for either the SEA Faculty or SEA Admin accounts? I assume Dr. Davis has them, but he's out today and I would like to finalize the setup before students are back on Monday.

Thank you,
Keith Lloyd-Davies

DoTS_UWRF

Dan Russell

Sharon Isern
Can students get access to the VM 2016 via seaphages.org? Or do they have to be logged in as faculty? We're in class right now. Thanks!!

Because of the software included, we couldn't post it totally publicly. And since there's no "registered student" accounts on PhagesDB, there's no way to give them access to the protected page.

That said, I'll email you (and any other faculty who want it) the magic link!

–Dan

Dan,

Would it be possible to share the link with me via email or message? I work in the IT department at UWRF with Karen Klyzek and the account we used previously (under Gary Knigge) is no longer active to download the SEALinux VM. We are working on rebuilding the image for the department laptops and need to download the file.

Thank you in advance,
Nate Overby
Division of Technology Services
UW-River Falls

jparker
Eureka! Exactly what I need. I have never seen that page. What menu is it under? I can't seem to be find a link for it on PhagesDB. Now that I know it exists, i'll bookmark it, but it would be good to know how to direct students to the page.
Thanks!
Jordan

jparker
Thanks Nick and cdshaffer! I only know enough coding language to frustrate myself, so I'll probably leave that to the experts. Is there a straightforward way to generate lists of pham members without opening the pham circle tool? This may be a more complicated question than can be easily answered here. I'm headed to the in silico workshop in two weeks, so I should be able to get more info there.
Thanks for your help!
Jordan