SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 24 Apr, 2017 16:18
DanRussell	Hi Sangha, From looking at the DNA Master file, I think that the longer of these two (which overlaps a lot of other tRNAs) is just a miscall. You can safely delete that one. The 425 bp one, however, is probably a tmRNA, and should be called. –Dan

Posted in: Gene or not a Gene → C1 phage

Link to this post \| posted 12 Apr, 2017 14:38
DanRussell	Shallee Page The last couple of days, I can't open the Lawrence Lab web page to download DNA master… Hi Shallee, This happens from time to time. Looks like the server has been reset and is working now. –Dan

Posted in: DNA Master → DNA Master failed update

Link to this post \| posted 04 Apr, 2017 17:44
DanRussell	Hi Nancy, These are probably tRNA genes, which don't appear in Phamerator (yet!). So for those you'll have to follow some of the tRNA guidelines rather than Starterator, Phamerator, etc. –Dan

Posted in: Phamerator → Missing Genes in Phamerator Ading_draft

Link to this post \| posted 28 Mar, 2017 14:29
DanRussell	Hi Victoria, If Phamerator ever prompts you for a password, it should just be: "phage". If that doesn't work, something else has gone wrong! –Dan

Posted in: SEA-PHAGES Virtual Machine → No Ubuntu 64-bit option when installing 2017 VM on Windows

Link to this post \| posted 02 Mar, 2017 20:27
DanRussell	Hi Nikki, Glad it worked. Definitely shutting down the VM or closing your computer while Phamerator's running/doing things can cause problems. I'd always advise to close Phamerator before shutting anything else down. –Dan

Posted in: Phamerator → Locked out of Phamerator

Link to this post \| posted 01 Mar, 2017 15:39
DanRussell	Hi Nikki, Did you try "phage" for the password? If phamerator ever wants a password, that's the one. If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here: It sounds like one of two things: your virtual machine is unable to access the internet your phamerator configuration file has become corrupted You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop. If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file: Steps to do this: Reboot the Virtual Machine Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.) Make sure Phamerator is NOT running. Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key) Paste in the following command: `mv ~/.phamerator/phamerator.conf ~/Desktop` Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft If prompted for a password, use: phage If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop. –Dan Edited 01 Mar, 2017 15:40

Link to this post | posted 01 Mar, 2017 15:39

DanRussell

Hi Nikki,

Did you try "phage" for the password? If phamerator ever wants a password, that's the one.

If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here:

It sounds like one of two things:
your virtual machine is unable to access the internet
your phamerator configuration file has become corrupted

You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop.

If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file:

Steps to do this:
Reboot the Virtual Machine
Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.)
Make sure Phamerator is NOT running.
Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key)
Paste in the following command:
mv ~/.phamerator/phamerator.conf ~/Desktop
Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft
If prompted for a password, use: phage
If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop.

–Dan

Edited 01 Mar, 2017 15:40

Posted in: Phamerator → Locked out of Phamerator

Link to this post \| posted 09 Feb, 2017 15:32
DanRussell	Note that there's also a little document on using Inkscape with Phamerator maps that came out of the Faculty Retreat last year: http://seaphages.org/faculty/information/#modifications http://seaphages.org/media/docs/UsingInkscapeToEditPhameratorMaps.pdf –Dan

Posted in: Phamerator → Printing phamerator maps

Link to this post \| posted 07 Feb, 2017 16:39
DanRussell	Hi Joe, As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example. Batch BLASTing in DNA Master As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams. (And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.) –Dan

Link to this post | posted 07 Feb, 2017 16:39

DanRussell

Hi Joe,

As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example.

Batch BLASTing in DNA Master

As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams.

(And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.)

–Dan

Posted in: DNA Master → BLASTing whole genome with "secure" connection

Link to this post \| posted 03 Feb, 2017 17:33
DanRussell	I think Chris is right here, and you unfortunately can't add Cluster info via GenBank file, which is the only input for PhamDB. So you're left with the option of locally modifying your database and adding in the clusters. The problem there is that if you then update the database using PhamDB, and your Phamerator imports the newly-updated version, you'll probably lose those changes and have to add them again. Not ideal! –Dan

Link to this post | posted 03 Feb, 2017 17:33

DanRussell

I think Chris is right here, and you unfortunately can't add Cluster info via GenBank file, which is the only input for PhamDB. So you're left with the option of locally modifying your database and adding in the clusters.

The problem there is that if you then update the database using PhamDB, and your Phamerator imports the newly-updated version, you'll probably lose those changes and have to add them again. Not ideal!

–Dan

Posted in: Phamerator → PhamDB: Make your own Phamerator databases

Link to this post \| posted 27 Jan, 2017 15:24
DanRussell	mavrodi So, just to clarify: if Step 1 fails then the only way to install SEA VM is to start changing BIOS settings? No other options available? I currently have five students in my class that can't install the 64-bit VM. Hi Dmitri, Yes, unfortunately the systems we tested the new VM on didn't have the no-64-bit-option issue, so we didn't anticipate this level of trouble. A second option would be to revert to the 2016 SEA VM, which is fairly similar and won't need much tweaking to be brought up-to-date. If you'd like links to the 2016 version, please email me! –Dan

Link to this post | posted 27 Jan, 2017 15:24

DanRussell

mavrodi
So, just to clarify: if Step 1 fails then the only way to install SEA VM is to start changing BIOS settings? No other options available? I currently have five students in my class that can't install the 64-bit VM.

Hi Dmitri,

Yes, unfortunately the systems we tested the new VM on didn't have the no-64-bit-option issue, so we didn't anticipate this level of trouble. A second option would be to revert to the 2016 SEA VM, which is fairly similar and won't need much tweaking to be brought up-to-date. If you'd like links to the 2016 version, please email me!

–Dan

Posted in: SEA-PHAGES Virtual Machine → No Ubuntu 64-bit option when installing 2017 VM on Windows

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