Link to this post | posted 01 Oct, 2019 15:30
DanRussell	As Chris says, there's not really a great way to acquire sequences in that way via the API. He's given a few options that would likely work. If you have just a request or two, however, you can email me (dar78@pitt.edu) and I can send them back to you. –Dan

Link to this post | posted 02 Jul, 2019 14:16
DanRussell	Hey Steve, The intent is to have that field represent protein-coding genes only. There are separate fields for tRNAs and tmRNAs, so that info would go there. We're actually working on making these fields auto-update when we do Phamerator updates so that they're consistent and in line with Phamerator. Right now they're manually entered, so they may be less reliable. –Dan

Link to this post | posted 25 Jun, 2019 15:32
DanRussell	I get this when trying to go to the Aragorn site: mbio-serv2.mbioekol.lu.se unexpectedly closed the connection. ERR_CONTENT_LENGTH_MISMATCH –Dan

Link to this post | posted 25 Feb, 2019 16:49
DanRussell	Deep kumar Hello All, I have made a PhamDB database of my genomes and now want to use phamerator but I do not see how to use phamerator? The standalone version is not supported anymore as I got to know. Thanks! Hi Deep, You need to contact Steve Cresawn (cresawsg@jmu.edu) and arrange to give him your database. He can make it available from the dropdown menu at phamerator.org. –Dan

Link to this post | posted 30 Jan, 2019 19:23
DanRussell	Hi Mitch, No, I don't think so. At least not in a productive manner. You would have to use a Wine or other emulator approach, and Chromebooks don't usually have the specs needed to run that kind of thing. Instead, you could partner the student with someone who has a functional DNA Master, and so one partner has DNA Master open, the other has Phamerator or GeneMark open. –Dan

Link to this post | posted 14 Jan, 2019 19:46
DanRussell	Hi Manuel, Did you follow our newest guide for installing DNA Master? https://phagesdb.org/media/docs/DNAMasterInstallationGuide.pdf It suggests that you install DNA Master in a location other than the /Program Files (x86)/ folder. That way you shouldn't run into the Administrator issues, which is still what those errors look like to me. –Dan

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