SEA-PHAGES | All posts created by c.sunnen

Link to this post \| posted 23 Nov, 2022 16:17
c.sunnen	Thanks, Debbie! I really just needed someone else to confirm this for me (or to tell me favored overlaps are a thing with integrases sometimes). Abysmal RBS it is (and yes, it is the best conserved of the options, even though it's not always the one called)!

Posted in: Choosing Start Sites → Integrase makes a 4bp overlap with immunity repressor?

Link to this post \| posted 23 Nov, 2022 14:20
c.sunnen	Hi all, We are annotating DY cluster phage Tarzan; there are only 5 members of this cluster, of which only 3 (Santhid, JoJo24, and Reyja) have been manually annotated. I am looking at the tyrosine integrase (gene 31 in Tarzan), and having trouble weighing the evidence for the best start. In short, I can call a favored 4bp overlap with the immunity repressor (gene 32) OR I can leave a gap and choose the start with the abysmal RBS (which is know is common for integrase genes). Are favorable overlaps also seen between integrase and immunity repressor if they're right next to each other? I seem to recall that integrase usually has an upstream gap… Some details: Starterator is not very helpful. Though there are 45 members of the pham, there is no real consensus; the most annotated start is only called 9/42 times (and only present in 22% of genes), and none of the phages in this cluster have it anyway. Within the cluster - which do look similar, but not identical - they all call different starts. However, while none of them called it, all 3 (Santhid, JoJo24, and Reyja) could have called a start that would've given a favorable 4bp or 8bp overlap with the immunity repressor. I've attached a summary of start options for each of these 4 genes (including Tarzan). Any insight would be appreciated. I'm leaning toward the 4bp overlap, but something tells me that's a "no no" for an integrase. 16Kb

Link to this post | posted 23 Nov, 2022 14:20

c.sunnen

Hi all,

We are annotating DY cluster phage Tarzan; there are only 5 members of this cluster, of which only 3 (Santhid, JoJo24, and Reyja) have been manually annotated. I am looking at the tyrosine integrase (gene 31 in Tarzan), and having trouble weighing the evidence for the best start. In short, I can call a favored 4bp overlap with the immunity repressor (gene 32) OR I can leave a gap and choose the start with the abysmal RBS (which is know is common for integrase genes). Are favorable overlaps also seen between integrase and immunity repressor if they're right next to each other? I seem to recall that integrase usually has an upstream gap…

Some details: Starterator is not very helpful. Though there are 45 members of the pham, there is no real consensus; the most annotated start is only called 9/42 times (and only present in 22% of genes), and none of the phages in this cluster have it anyway. Within the cluster - which do look similar, but not identical - they all call different starts. However, while none of them called it, all 3 (Santhid, JoJo24, and Reyja) could have called a start that would've given a favorable 4bp or 8bp overlap with the immunity repressor. I've attached a summary of start options for each of these 4 genes (including Tarzan).

Any insight would be appreciated. I'm leaning toward the 4bp overlap, but something tells me that's a "no no" for an integrase.

Posted in: Choosing Start Sites → Integrase makes a 4bp overlap with immunity repressor?

Link to this post \| posted 10 Sep, 2022 17:36
c.sunnen	For anyone that may be helped by this, installing that library worked like a charm!

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 10 Sep, 2022 16:30
c.sunnen	Hmmmm. I wonder if I'm having this issue. I've tried BLASTing a single gene, and now I get the error "Could not load SSL library." I'll try the fix below, and let everyone know if it works. Nikki hgavin90 DanRussell Hi Katie, I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked. ~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~ UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again. https://phagesdb.org/static/vcredist_x86.exe Hopefully that helps, –Dan Nevermind – changing secure connection did not work but this installation recommended by Dann has. Woo!

Link to this post | posted 10 Sep, 2022 16:30

c.sunnen

Hmmmm. I wonder if I'm having this issue. I've tried BLASTing a single gene, and now I get the error "Could not load SSL library."

I'll try the fix below, and let everyone know if it works.

Nikki

hgavin90
DanRussell
Hi Katie,

I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked.

~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~

UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again.

https://phagesdb.org/static/vcredist_x86.exe

Hopefully that helps,
–Dan

Nevermind – changing secure connection did not work but this installation recommended by Dann has. Woo!

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 10 Sep, 2022 12:52
c.sunnen	Veronique, Did this ever fix for you? It looks like I might be having the same issue. It's almost as if DNA Master just didn't even start sending queries. It stayed at 0% overnight with no progress. Is this what happened for you? Nikki

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 03 Jun, 2022 21:08
c.sunnen	Thank-you, Christian! I see that now in my flat file. It's weird though, because the DNA Master file has "tRNA-Ile2(cat)" in the product field (and properly in the Documentation), so I don't know why it's getting changed in the flat file. Maybe I can just edit the flat file directly and resubmit; the sub file appears accurate. Thank-you! Nikki

Posted in: tRNAs → Met vs Ile2

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

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?

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

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