SEA-PHAGES | All posts created by stpage

Link to this post \| posted yesterday, 08:51
stpage	mthomas There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this? Can you post the HHPRED coverage and percent identity? What do you get when you do an amino acid sequence alignment against the SAM lyase from T3?

Link to this post | posted yesterday, 08:51

mthomas
There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this?

Can you post the HHPRED coverage and percent identity? What do you get when you do an amino acid sequence alignment against the SAM lyase from T3?

Posted in: Cluster ED Annotation Tips → SAM lyase ?

Link to this post \| posted 03 Apr, 2025 16:38
stpage	Hi, here is a student tutorial I wrote for the Genome Education partnership. If you have any questions or suggestions, drop me an email! 1.33Mb

Posted in: Annotation → Alphafold tutorial

Link to this post \| posted 03 Mar, 2025 19:41
stpage	Hi is there a standard protocol for reviving phage from -80 stocks? Well, I assume there is. What I mean is, what do y'all recommend?

Posted in: Phage Discovery/Isolation → Reviving

Link to this post \| posted 22 Jan, 2025 20:42
stpage	Our A.glob lawns are often like that but we have been using top agar from early in last semester. We'll give that a try. Thanks, Vic!

Posted in: Phage Discovery/Isolation → Plaques appear on spot test, don't appear in titer

Link to this post \| posted 22 Jan, 2025 19:10
stpage	So, we have had a lot of trouble amplifying, with great spot tests and poor plaque assays (a lot of killing at high concentration but no nice plaques at any concentration). I suspect lysis from without. So, after checking to make sure that we are plating from a single colony of the correct host, what would be the next step? Some spot test plate pictures attached. Edited 22 Jan, 2025 19:11 2.41Mb 2.44Mb

Link to this post | posted 22 Jan, 2025 19:10

stpage

So, we have had a lot of trouble amplifying, with great spot tests and poor plaque assays (a lot of killing at high concentration but no nice plaques at any concentration). I suspect lysis from without. So, after checking to make sure that we are plating from a single colony of the correct host, what would be the next step?
Some spot test plate pictures attached.

Edited 22 Jan, 2025 19:11

Posted in: Phage Discovery/Isolation → Plaques appear on spot test, don't appear in titer

Link to this post \| posted 28 May, 2024 12:03
stpage	Ok, thanks.

Posted in: SMART Function Investigations → spanins

Link to this post \| posted 23 May, 2024 18:53
stpage	Has anyone done a deep dive on phage spanins? Is it worth looking at or would we need some wetlab support anyway? Shallee

Posted in: SMART Function Investigations → spanins

Link to this post \| posted 29 Dec, 2023 14:00
stpage	I am trying to get my fastq files into the VM. They seem to be too large to email. I think I followed these instructions for shared folders and I did choose "auto-mount" can see the shared folders but they did not appear in the /Media folder. I updated the virtual machine for Newbler but the shared folders are not under media or desktop or home. I tried searching the whole computer with no success. They are visible in the VM screen in a bottom icon for shared folders (which doesn't show in the screenshot) but…. I tried a couple of online help forums. Seems to be a mounting problem maybe? So I tried following the directions at: https://vineetcic.medium.com/how-to-access-folders-on-ubuntu-host-machine-from-an-ubuntu-virtual-machine-in-virtualbox-a020a9dbc5a4 but I am not at all sure that I did it correctly in command line. Thanks, Shallee —————————————————– cdshaffer easy way (that I use in class when time is an issue) I tell student: open browser, connect to email, send files to yourself as attachment. Bonus feature: automatic backup of files. If you need to move many files back and forth: 1. make sure you are using a recent version of Virtualbox and have installed guest additions in the ubuntu machine 2. with machine off go to settings -> shared folder 3. click the tiny folder with the plus sign to add a shared folder 4. in the folder path entry click the arrowhead and select "other" 5. select the mac Desktop folder to share between guest and host 6. select the "Make permanent" setting so you only have to do this once. 7. The shared folder will be in the /media folder in the guest which is in the top level of folders (i.e. two folders up from your home folder). The name of the folder inside the guest machine will be something like sf_Desktop 8. Files placed in there will appear on the Desktop of your mac You an also set up drag'n'drop to supposedly be able to move files back and forth but I have had less success with that technique EDIT 1/11/24: Ok, didn't get drag'n'drop to work but got the files in with the SharedFolder bit. I suspect my filepaths were wrong…. Edited 11 Jan, 2024 18:27

Link to this post | posted 29 Dec, 2023 14:00

stpage

I am trying to get my fastq files into the VM. They seem to be too large to email.

I think I followed these instructions for shared folders and I did choose "auto-mount" can see the shared folders but they did not appear in the /Media folder. I updated the virtual machine for Newbler but the shared folders are not under media or desktop or home. I tried searching the whole computer with no success. They are visible in the VM screen in a bottom icon for shared folders (which doesn't show in the screenshot) but….
I tried a couple of online help forums. Seems to be a mounting problem maybe? So I tried following the directions at: https://vineetcic.medium.com/how-to-access-folders-on-ubuntu-host-machine-from-an-ubuntu-virtual-machine-in-virtualbox-a020a9dbc5a4 but I am not at all sure that I did it correctly in command line.

Thanks,
Shallee

—————————————————–

cdshaffer
easy way (that I use in class when time is an issue) I tell student: open browser, connect to email, send files to yourself as attachment. Bonus feature: automatic backup of files.

If you need to move many files back and forth:
1. make sure you are using a recent version of Virtualbox and have installed guest additions in the ubuntu machine
2. with machine off go to settings -> shared folder
3. click the tiny folder with the plus sign to add a shared folder
4. in the folder path entry click the arrowhead and select "other"
5. select the mac Desktop folder to share between guest and host
6. select the "Make permanent" setting so you only have to do this once.
7. The shared folder will be in the /media folder in the guest which is in the top level of folders (i.e. two folders up from your home folder). The name of the folder inside the guest machine will be something like sf_Desktop
8. Files placed in there will appear on the Desktop of your mac

You an also set up drag'n'drop to supposedly be able to move files back and forth but I have had less success with that technique

EDIT 1/11/24: Ok, didn't get drag'n'drop to work but got the files in with the SharedFolder bit. I suspect my filepaths were wrong….

Edited 11 Jan, 2024 18:27

Posted in: SEA-PHAGES Virtual Machine → Shared folders

Link to this post \| posted 30 Mar, 2023 16:11
stpage	Official function list (2023) "we are no longer using "capsid morphogenesis protein""

Posted in: Functional Annotation → Capsid morphogenesis protein

Link to this post \| posted 30 Mar, 2023 12:46
stpage	Looks like these have been fixed @ NCBI but not in SEA-PHAGES…? 9Kb

Posted in: Cluster DC Annotation Tips → capsid maturation proteases

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