Link to this post | posted 16 Feb, 2022 20:34

c.sunnen

Update and new question. I have several students that have successfully installed Parallels and Windows 11 (for some reason, Windows 10 was not a choice for most of them, but was for our first student install - go figure). I successfully convinced our institution to pay for a handful of licenses for the year! But now students are having issues getting DNA Master to work properly. Errors seem to abound when trying to download onto the "Windows" desktop. Also, creating shortcuts doesn't seem to work (it throws errors), but starting directly out of the folder it was downloaded into works. We've had success downloading into "C," "ProgramFiles(x86)" and running it directly out of there. BUT I have a couple of students that can't successfully uninstall previous attempts that downloaded elsewhere, so they can't do new installations into the proper place. All attempts to search for files, delete, and empty the recycle bin (in both the Windows and the Mac) isn't sufficient; new DNAMaster downloads still only give options to "repair," "modify," or "uninstall," and then the uninstall doesn't work. Any help or insight would be greatly appreciated! How can we get old (likely fragmented) versions of DNA Master off of these Parallels/Windows11 machines so we can get new installations? Thanks! Nikki @ USciences

Link to this post | posted 20 Jan, 2022 01:24
c.sunnen	Any updates on using either Parallels or Wine (or some other work around)? I've got a couple TAs that have also encountered this, and I anticipate I'll have several students as well… I'll share if I get updates on making it work! Thanks! Nikki

Link to this post | posted 12 Jan, 2022 21:04
c.sunnen	Thanks for this! We're already using your 2019 paper, "A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation," in class as an introduction to both annotation and reading the primary literature. Yay! Nikki

Link to this post | posted 10 Jan, 2022 18:29

c.sunnen

Hello! This may be of interest to faculty/instructors/grad students. Please see the request and course info below, that comes from a colleague at Rowan University. Share as you see fit, as this position is for THIS spring semester! If interested, please contact Dr. Grace Farber, Associate Dean of Program Development, College of Science and Mathematics, Rowan University: farber@rowan.edu, 856-256-4344 Rowan is in dire need of an adjunct. The course can be run as the instructor sees fit and remotely (running WF 9:30am-12:15pm). The previous instructor was using curriculum from https://thegep.org/ although we are trying to figure out which one. Please let me know if you have any individuals you think might be interested and thank you!! BIOL 01459 - Genome Sciences This laboratory course provides the student with a survey of the highly interdisciplinary field of Genome Sciences. Students will engage critically with the primary literature to master concepts in topics including genome sequencing technology and analysis, comparative and evolutionary genomics, structural genomics, environmental and conservation genomics,and genomics in human health and disease. Students will additionally have the opportunity to directly collect and analyze genomic data using state-of-the-art methods. 4.000 Credit hours

Link to this post | posted 10 Sep, 2021 18:25
c.sunnen	And this is why we love you, Vic. You have all the answers! Thanks for clarifying this for us! I hope it's useful for others, too! Nikki

Link to this post | posted 10 Sep, 2021 16:36

c.sunnen

So after running this course for 6+ years, I discovered that my colleague and I clean-up our benches differently at the end of lab, and we both swear we were taught (during the same training) the way we each do it is "correct." Whenever disinfecting BEFORE lab, we always do Ci-decon first, let it dry, followed by 70% Ethanol. The question is whether the order should be reversed at the end of experiments, before leaving the lab. Should it remain Ci-decon first, then EtOH? Or should it be EtOH first, followed by Ci-decon? Does it matter? (and if it does matter, can you share why?)

Link to this post | posted 24 May, 2021 21:53
c.sunnen	Thanks, Debbie! That was the issue. Interestingly, I wasn't missing any of the files in the Blast folder, it was mostly .VAL files in the Blank Genome folder. I guess somewhere it got corrupted (either before or after I tried to BLAST it). Hurray! Nikki

Link to this post | posted 24 May, 2021 19:11

c.sunnen

Hello! So I've got 2 predicted tRNAs by both tRNAScanSE and Aragorn, in cluster E phage, Filch. One of them is canonical and easy to call (tRNA-Gly(tcc)). The other, just upstream, has a 3bp intron (gcc) according to Aragorn. According to tRNAScanSE (Infernal score = 36.3), it can't determine the anticodon. I would simply leave it out, except it seems that several other phages have called this one, BUT haven't used the anti-codon specified by Aragorn, though they have kept the coordinates. according to Aragorn's prediction. For example, like Filch, CrystalP's Aragorn output predicts an 84bp tRNA (81+3bp intron)at coordinates 63089-63172: tRNA-Lys(ctt). But in GenBank, at these same coordinates it's "tRNA-Arg (cct)" What is happening, and what should I do? Note that CrystalP is the most recently annotated phage in this cluster to call tRNAs at all. Other phages in this cluster, annotated more recently (like Quallification) have tRNAs in the same region (according to online Aragorn), but were never called (even the canonical one). I've attached the Aragorn output for Filch (note that the very first one it calls isn't real, as it's in the middle of an ORF). 3Kb

Link to this post | posted 24 May, 2021 13:49

c.sunnen

So this is a new one. I'm BLASTing a whole genome (Filch, cluster E) through DNAMaster in order to QC it. I've done it four times now, and every time, it completes (overnight BLAST), but when I go to save it under a new name, when I open the new file all of the BLAST data is gone. This has happened on two different PCs, regardless of whether or not I recreate the documentation after BLASTing. Right now, I'm simply not closing the BLASTed file on my laptop, and working on an unBLASTed version on my desktop to QC! Has anyone else encountered this? I'm running the most recent update of DNAMaster (on both machines): Version 5.23.6, Build 2700, May 11 2021 Thanks! Nikki

Link to this post | posted 24 May, 2021 13:38
c.sunnen	I had this problem also (didn't fix it yet). But I was able to "export" the six-frame translation into a Word doc, and used that.