Link to this post | posted 20 Mar, 2020 01:20
DanRussell	Hi Dan and D'Andrew, Interesting. I can tell you (as the person who programmed the button on PhagesDB) that the same exact request is sent to GeneMark in both the Mayweather and Kenosha cases. So it must be GeneMark itself that is making a decision about which model/method to use. From the PhagesDB perspective, we don't distinguish based on length or anything. –Dan

Link to this post | posted 06 Feb, 2020 17:48

DanRussell

Hi Roy, I think you've caught things between versions of the Phamerator database. If you go to phamerator.org and click on the little dropdown database menu in the top left, it'll show you what version of the database you're currently viewing. As of now, I see Actino_Draft version 338. Meanwhile, Chris has recently made a link where you can check the version of the database Starterator is using. http://phages.wustl.edu/starterator/database.version Earlier today, it showed 337, but I just checked again and now it's showing 338, so hopefully things are back in sync now. –Dan

Link to this post | posted 06 Feb, 2020 16:16
DanRussell	Hi guys, For the record, here's a link to the Genome Announcement we wrote after sequencing that host. https://www.ncbi.nlm.nih.gov/pubmed/27013048 –Dan

Link to this post | posted 05 Feb, 2020 19:15
DanRussell	Hi Amy, You don't need to directly address it during your annotation, but it can be interesting to work with the students and see how that might affect the protein(s) in question. We also add those sequencing notes as sometimes they can help explain an odd phenotype (turbid AND clear plaques, e.g.). –Dan

Link to this post | posted 24 Jan, 2020 15:20
DanRussell	I think Chromebooks are a non-starter as far as DNA Master is concerned, but you can always pair a Chromebook user (who can still access Phamerator, GeneMark, PECAAN, etc.) with another student who has functional DNA Master. I've been successfully using DNA Master on a Windows 10 virtual machine for a while now, following the instructions here. –Dan

Link to this post | posted 21 Jan, 2020 15:48
DanRussell	Hi Fernando, Are you on a University/computer lab computer? Could it be that the system is somehow doing a regular cleanup operation to remove "unwanted" stuff and somehow DNA Master is getting caught in that? If so, it'd probably be easiest for your local IT to sort out. I have DNA Master installed on a Windows 10 virtual machine, and it's been stable for months. –Dan

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