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All posts created by DanRussell

| posted 12 Jun, 2018 12:59
Hey Germán,

Since this one was sequenced a while ago, I think I should probably check the sequence in this region to see if it's a sequencing error. I'll get to that ASAP.

–Dan
Posted in: Frameshifts and IntronsNew frameshift in an A1 phage?
| posted 04 Jun, 2018 21:12
Hi Ann,

I'm not sure there is. My recent experiences with WINE have varied, and almost always the size of the genome is a determining factor in how well WINE works. A 50 kb genome loads in a few seconds, but a 100 kb genome never works.

Not helpful, obviously, but others may have better suggestions.

You may be able to request a loaner laptop for the workshop. I'd ask Vic and/or Billy.

–Dan
Posted in: DNA MasterAnnotating Cluster C1 phage onn Macbook Pro
| posted 26 Apr, 2018 13:55
Hi Andrea,

As Debbie said, the "master" copy of Phamerator gets updated about once a week. PhagesDB checks every night to see if a new version exists and if so, installs it. Online Phamerator does the same, but might not check every night, which is why things may appear out-of-sync for a day or two. But thanks for letting us know, and I'll double-check that everything is working as intended.

–Dan
Posted in: Web PhameratorPham Number Discrepancy
| posted 27 Feb, 2018 16:55
FROM AN NIH LIST

Dear All,

An ORISE fellow position is available in my laboratory for a project involving virology and bioinformatics knowledge including computer language. This position provides a training opportunity for enthusiasts interested in developing bioinformatics tools and databases for virus detection, annotation, and characterization. The overall goal of the project is cell line and vaccine safety.

Individuals that meet the requirements should submit their CV and contact information for three references.

Thank you.

Regards,
Arifa Khan
Supervisory Microbiologist
Laboratory of Retrovirus Research
Division of Viral Products
Office of Vaccines Research and Review
Center for Biologics Evaluation and Research
U.S. Food and Drug Administration
10903 New Hampshire Ave
Bldg. 52-72, Room 1216
Silver Spring, MD 20993
Tel no. 240-402-9631
Email: arifa.khan@fda.hhs.gov
Posted in: General Message BoardORISE Fellow Position at FDA
| posted 26 Jan, 2018 20:48
GregFrederick@letu.edu
We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail.

We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis.

I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you.

Thoughts? Is it a server problem, something with our genome annotation or something else?

Thanks. greg

Hi Greg,

To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results?

BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on?

–Dan
Posted in: DNA MasterAuto-annotation fix for fall 2017 and later
| posted 26 Jan, 2018 20:46
ptsourkas
Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure".

Thanks,
Philippos

Hi Philippos,

Is your DNA Master up to date? If you run Update does all look good? Any other weird errors popping up?

I think the servers are working. You've entered the proper access code in the linked document?

–Dan
Posted in: DNA MasterAuto-annotation fix for fall 2017 and later
| posted 22 Jan, 2018 20:04
Steven Caruso
Those of us who use any of the alternate hosts still have to use the VM, sadly.

Steve

For now! I know the other Steve C. is working on having multiple databases available online, so at some point that will no longer be the case.

–Dan
Posted in: SEA-PHAGES Virtual MachineStudent download of 2016 VM
| posted 22 Jan, 2018 19:59
Randall DeJong
Dan Russell,
I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit?

Cal Keen
ckeen@calvin.edu

Hi Cal,

Did you see my email response? In short: we're not recommending that you install the Virtual Machine at all this year, unless you have a specific need for it. Do you want to proceed with installing anyway?

–Dan
Posted in: SEA-PHAGES Virtual MachineStudent download of 2016 VM
| posted 17 Jan, 2018 17:58
Hi Claire,

I just added a "Last modified" date to the Google Sheet. It should auto-update anytime the list is changed and saved. The date itself is in cell B1.

Hope that helps!
–Dan
Posted in: Request a new function on the SEA-PHAGES official listApproved list
| posted 17 Jan, 2018 17:56
I think perhaps our servers were just down around Jan 12. Is it working now?

–Dan
Posted in: DNA MasterAuto-annotation fix for fall 2017 and later