Link to this post | posted 08 Jan, 2019 17:08
DanRussell	Hi Rick, The "Finish" button of the installer has a checkbox that says something like "Launch DNA Master now?", but even if checked it won't actually launch DNA Master. You'll still need to open it by locating the correct icon in the folder where it was installed. –Dan

Link to this post | posted 08 Dec, 2018 03:00

DanRussell

Hi. Instead of using WINE on your Mac, you might want to follow our new directions to get a Windows virtual machine set up (free) and install DNA Master on that. The "Operating System" section on the page below contains a link to the guide for getting the Windows virtual machine, and then the Installation section contains the info for how to install DNA Master. https://phagesdb.org/DNAMaster/ Good luck, –Dan

Link to this post | posted 19 Nov, 2018 17:51

DanRussell

Hi Bill, Since BabeRuth sounds like the outlier here, I went back and took a look at the BabeRuth sequencing data. Here's a pic of that region. Very solid coverage and agreement that there are indeed 5 Cs here, not 4 like the others with similar genomes. This is a real biological feature, not a sequencing error! I can't say for sure of course whether this is really a frameshift (in which case the protein would still be made) or just a mutation that truncates the protein (more likely), but the underlying DNA sequence at least is correct. Good eye, and this is definitely the kind of thing that's worth checking. –Dan

Link to this post | posted 26 Jun, 2018 20:18

DanRussell

Hey Germán, I was able to find the original data for Anglerfish on one of our old machines. Turns out it is indeed a sequencing error. About 50% of the reads had 4 Cs instead of 3 Cs there, but the consensus was called with 3 Cs. Since it was sequenced in the early days of Ion Torrent, we weren't as good at picking up those errors, but after that definitely confirmed that in cases like that, the longer string was correct. I've added a fourth C to that position in the PhagesDB fasta file. I'll be in touch via email about how to move your existing annotation info to the new sequence. –Dan

Link to this post | posted 15 Jun, 2018 15:53

DanRussell

Pollenz Thanks Dan, the version i have is updated, but where do i see the info above about the build, i dont see it in the preferences. I can say that the secure window does not look exactly like the notes I saw as its missing one of the check boxes. I also am getting a "cant load SSL library when I tried to blas a single gene. Ah, SSL error. Did you see this? https://seaphages.org/forums/topic/4436/?page=1#post-5805 –Dan

Link to this post | posted 13 Jun, 2018 15:04
DanRussell	Hi Rick, Did you update DNA Master? Try running an update. (Help–>Update DNA Master) Then restart and check your version. (Help–>About) The latest version is: Version 5.23.2 Build 2583 15 May 2018 –Dan

Link to this post | posted 12 Jun, 2018 12:59
DanRussell	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

Link to this post | posted 04 Jun, 2018 21:12
DanRussell	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

Link to this post | posted 26 Apr, 2018 13:55
DanRussell	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

Link to this post | posted 27 Feb, 2018 16:55

DanRussell

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