Link to this post | posted 17 Sep, 2020 19:22

DanRussell

Hi Tiara, There are basically two steps to getting DNA Master to work on a Mac. The first is getting a functioning version of Windows installed in VirtualBox. I think that's the problem with the first error in your document. The other errors are related to step 2, installing DNA Master, which will be impossible if you haven't completed step 1. For step 1 (getting Windows running) are you carefully following the instructions in this document? https://phagesdb.org/media/docs/InstallingWindowsOnMac.pdf –Dan

Link to this post | posted 02 Sep, 2020 18:51
DanRussell	Hi Tiara, I haven't encountered that myself before, but perhaps the suggestions on this page will help: https://medium.com/@DMeechan/fixing-the-installation-failed-virtualbox-error-on-mac-high-sierra-7c421362b5b5 –Dan

Link to this post | posted 19 Aug, 2020 20:00
DanRussell	Hey Steve, Seems to be working fine for me at the moment. –Dan

Link to this post | posted 09 May, 2020 20:35
DanRussell	Hi Fernando, No, "None" just means we haven't made a determination for that cluster yet, so it could be either. Some of the clusters are very well known at this point, while others are fairly new and we haven't taken a close look. –Dan

Link to this post | posted 09 Apr, 2020 00:23

DanRussell

Hi Susanne, The length disparity is almost certainly because of the terminal repeat. When I assembled your genome, it looked clear to me that your it had direct terminal repeats; there was an area of approximately double coverage (compared to the rest of the genome) and flanking reads that started on the same base. That's classic terminal repeat. In those cases, we generally report the genome with the terminal repeat on each end, as the DNA would actually appear in the phage capsid. The Metroid terminal repeat is around 10kb, which almost certainly accounts for the difference between your assembly and the final file. My initial assembly was also only ~140 kb, but once I added the second copy of the repeat, it went to ~150kb. Hope that makes sense, –Dan

Link to this post | posted 05 Apr, 2020 15:39
DanRussell	Hi Kyle, Here are a couple options: Sherwood Casjens' paper about using terminases to determine end types, but it also sort of explains what the ends types might be: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082370/ A more recent paper about the program PhageTerm, which tries to predict end type from sequencing reads: https://www.nature.com/articles/s41598-017-07910-5 Take care, –Dan

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