SEA-PHAGES | All posts created by c.sunnen

Link to this post \| posted 03 Jun, 2022 13:53
c.sunnen	I am attempting to submit C1 phage Jedediah, but when it goes through the file checker, I get the following error: ERROR: Evaluation ID: TRNA-EVAL-011. Status: error. Definition: Check that the annotated amino acid is consistent with the prediction(s) made by Aragorn and/or tRNAscan-SE for SEA_JEDEDIAH_180 (Jedediah_TRNA_24). The tRNA feature is expected to have a correct isotype (amino acid) prediction. Result: The annotated isotype (Ile) is inconsistent with Aragorn (Met) and tRNAscan-SE (Ile2). Status was changed from 'warning' to 'error' automatically due to no interactivity. The problem is, it IS annotated as Ile2, not Ile. I even re-typed it to be sure. The Bioinformatics Guide says to annotate this as Ile2 (tRNAScan's call, not Aragorn's call of Met), but I also see that other C1s, such as Khaleesi, TinyTim, and McWolfish all call this Met. I re-ran Khaleesi through tRNAScan-SE, and it also calls this Ile2, even though the final GenBank version calls it Met. What am I missing? Should I call this Met?

Link to this post | posted 03 Jun, 2022 13:53

I am attempting to submit C1 phage Jedediah, but when it goes through the file checker, I get the following error:

ERROR: Evaluation ID: TRNA-EVAL-011. Status: error. Definition: Check that the annotated amino acid is consistent with the prediction(s) made by Aragorn and/or tRNAscan-SE for SEA_JEDEDIAH_180 (Jedediah_TRNA_24). The tRNA feature is expected to have a correct isotype (amino acid) prediction. Result: The annotated isotype (Ile) is inconsistent with Aragorn (Met) and tRNAscan-SE (Ile2). Status was changed from 'warning' to 'error' automatically due to no interactivity.

The problem is, it IS annotated as Ile2, not Ile. I even re-typed it to be sure. The Bioinformatics Guide says to annotate this as Ile2 (tRNAScan's call, not Aragorn's call of Met), but I also see that other C1s, such as Khaleesi, TinyTim, and McWolfish all call this Met. I re-ran Khaleesi through tRNAScan-SE, and it also calls this Ile2, even though the final GenBank version calls it Met.

What am I missing? Should I call this Met?

Posted in: tRNAs → Met vs Ile2

Link to this post \| posted 22 Feb, 2022 22:46
c.sunnen	Oops! Thanks Eric. I updated the sharing settings. Try it now. Also, a FANTASTIC TA of mine, Mayra Rosales (who also works in IT part-time), found a great resource for those of us that had issues uninstalling DNA Master (in order to reinstall into the correct place). You can access it here: http://www.uninstallhelps.com/how-to-uninstall-dna-master-5-22-1-build-2307.html There are 7 different methods to try, one of which is an "Auto-uninstall" button at the bottom that you can also try. She also recommends going into the Control Panel to uninstall from there. Edited 22 Feb, 2022 22:51

Link to this post | posted 22 Feb, 2022 22:46

c.sunnen

Oops! Thanks Eric. I updated the sharing settings. Try it now.

Also, a FANTASTIC TA of mine, Mayra Rosales (who also works in IT part-time), found a great resource for those of us that had issues uninstalling DNA Master (in order to reinstall into the correct place). You can access it here: http://www.uninstallhelps.com/how-to-uninstall-dna-master-5-22-1-build-2307.html There are 7 different methods to try, one of which is an "Auto-uninstall" button at the bottom that you can also try. She also recommends going into the Control Panel to uninstall from there.

Edited 22 Feb, 2022 22:51

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 22 Feb, 2022 22:30
c.sunnen	Update! I created a little protocol for how to download and install DNA Master on Windows 11 (in Parallels). I've found it's critical not to make a shortcut and to download it directly to the Program Files (x86) location. These instructions can be found here: https://docs.google.com/document/d/1YNqYrnjzNkVGNv-gjxvrX_8_sIWuxDqXc_ZPLREhYfI/edit?usp=sharing I hope this is helpful to others! Let me know if it does/doesn't work for you.

Link to this post | posted 22 Feb, 2022 22:30

c.sunnen

Update!

I created a little protocol for how to download and install DNA Master on Windows 11 (in Parallels). I've found it's critical not to make a shortcut and to download it directly to the Program Files (x86) location. These instructions can be found here:
https://docs.google.com/document/d/1YNqYrnjzNkVGNv-gjxvrX_8_sIWuxDqXc_ZPLREhYfI/edit?usp=sharing

I hope this is helpful to others! Let me know if it does/doesn't work for you.

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 22 Feb, 2022 17:14
c.sunnen	Thanks everyone. It is now working on my end. I have no idea why you'd be getting a message that you don't have WiFi. Nikki

Posted in: Phamerator → Phamerator not loading

Link to this post \| posted 21 Feb, 2022 19:17
c.sunnen	Thank-you both! Hopefully someone will post soon with a solution! I wonder if I could access it the old-fashioned way in Ubuntu. If I get the chance, I'll try it and let you all know if it worked.

Posted in: Phamerator → Phamerator not loading

Link to this post \| posted 21 Feb, 2022 13:30
c.sunnen	Hi all, Is anyone else having trouble accessing Phamerator? It started for me on Friday, and I figured it was just updating, but I still can't access this morning. Tried 2 different browsers, and it just doesn't load. I get "HTTP ERROR 502." Is it just me? I wanted to teach translational frameshifts this week, which will be tricky without Phamerator! Thanks! Nikki @ USciences

Posted in: Phamerator → Phamerator not loading

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 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

Posted in: DNA Master → DNA Master on M1 Mac

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

Posted in: DNA Master → DNA Master on M1 Mac

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

Posted in: General Message Board → New annotation software

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 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

Posted in: General Message Board → Adjunct in Genome Sciences (remote) position

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