Link to this post | posted 17 Dec, 2019 18:39

DanRussell

Hi Evan, It seems like that Starterator report is now updated. My guess is that you did indeed catch it when the databases were slightly out-of-sync, since a new database version was posted last night. Usually when this happens it's just a matter of waiting for one of the tools to finishing processing, but we'll try to find a way to keep everything more in sync from here on. Can you access it now successfully? –Dan

Link to this post | posted 20 Nov, 2019 14:52
DanRussell	Hi D'Andrew, Have you tried the steps outlined in this document? https://phagesdb.org/media/docs/InstallingWindowsOnMac.pdf We definitely recommend running a Windows virtual machine if possible rather than using Wine, since it's much more likely to work smoothly. –Dan

Link to this post | posted 07 Nov, 2019 18:17

DanRussell

Hi Amanda, Awesome that 1) your students are reading papers like this and 2) that they noticed that obvious discrepancy! You'll notice that the label on D29's phage page actually says "Cluster Life Cycle" (rather than "Phage Life Cycle" or something like that). When deciding how to list life cycle information on the site, we had to choose between listing each phage's life cycle (which we wouldn't really know for the vast majority except for bioinformatic predictions, and would be much more onerous to maintain) or each cluster's typical life cycle. We chose the latter as a quick way to classify typical behavior, but with the caveat that not all phages in a cluster will fit with the norm. So D29 has the "Cluster Life Cycle" as "Temperate" because almost all Cluster A phages are, in fact, temperate. But it's one of the atypical Cluster As as you described. In fact, when Graham wrote the original D29 paper, he hypothesized that it had recently lost its lysogeny machinery and there were phages that would look very similar but with that machinery still intact. So when StarStuff was sequenced years later, it was a great confirmation! If you go to the Cluster A page, there's some language that summarizes this in the "Lysogeny Notes" section, mentioning that caveat. Hope that all makes sense! –Dan Edited 07 Nov, 2019 18:19

Link to this post | posted 01 Oct, 2019 16:10
DanRussell	Hi Steve, We usually try to get to these daily, but sometimes other things crop up and they slide for a little while. You can always prompt Debbie or me if you've been waiting a couple days, as we've probably just been distracted and will get back to it ASAP. We won't be offended. –Dan

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