SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 22 Jun, 2016 20:37
DanRussell	Hi Eric, I'll add what I know and then pass it along. - I am aware of the C cluster myoviruses. Are there more clusters of myoviridae among the mycobacteriophages? Until this past year, all known Mycobacteriophages that were Myoviridae were in Cluster C. But Hope College discovered Phrappucino, the only other Myoviridae we've collectively found. It's a Singleton. - Finally, is there a lysogen containing a C cluster phage and does it contain a classical prophage integration? Though there have been some attempts, I don't think anyone has isolated and verified a Cluster C lysogen. There are some suspected Cluster C lysogens I've heard about, but I don't think anyone's gone as far as verifying that there are integrated genomes. There's no obvious bioinformatic evidence that they'd be temperate, and all of our attempts at isolating Cluster C lysogens at Pitt have been unsuccessful. - Is there a myoviridae phage that aligns most closely with a syphoviridae cluster and is thus an "odd one out", primarily due to its tail structure? From Welkin: no. They're different enough that we haven't seen that situation yet in the Mycobacteriophages. - Has anyone compared the tail proteins of the two morphotypes of mycobacterial phages? How about a comparison of the head-tail connectors? Portal proteins? Terminases? Also from Welkin: not that we know of, at least in a comprehensive way. –Dan

Link to this post | posted 22 Jun, 2016 20:37

Hi Eric,

I'll add what I know and then pass it along.

- I am aware of the C cluster myoviruses. Are there more clusters of myoviridae among the mycobacteriophages?

Until this past year, all known Mycobacteriophages that were Myoviridae were in Cluster C. But Hope College discovered Phrappucino, the only other Myoviridae we've collectively found. It's a Singleton.

- Finally, is there a lysogen containing a C cluster phage and does it contain a classical prophage integration?

Though there have been some attempts, I don't think anyone has isolated and verified a Cluster C lysogen. There are some suspected Cluster C lysogens I've heard about, but I don't think anyone's gone as far as verifying that there are integrated genomes. There's no obvious bioinformatic evidence that they'd be temperate, and all of our attempts at isolating Cluster C lysogens at Pitt have been unsuccessful.

- Is there a myoviridae phage that aligns most closely with a syphoviridae cluster and is thus an "odd one out", primarily due to its tail structure?

From Welkin: no. They're different enough that we haven't seen that situation yet in the Mycobacteriophages.

- Has anyone compared the tail proteins of the two morphotypes of mycobacterial phages? How about a comparison of the head-tail connectors? Portal proteins? Terminases?

Also from Welkin: not that we know of, at least in a comprehensive way.

–Dan

Posted in: Phage Biology → Myo, Sypho and terminase

Link to this post \| posted 10 May, 2016 14:13
DanRussell	Matt Benczkowski Hi Dan, I am a Pitt student and my computer was wiped clean in March, but I still need the software, could you please send me the Mac SEA VM file? Thank you! Matt Benczkowski msb82@pitt.edu Just sent it to you, Matt. –Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 21 Apr, 2016 19:23
DanRussell	Aaron Stevens Hey Dan, I am a student working on a phage project outside of class with a partner. Would you ba able to send the links for the SEA VM file for windows? Thanks, Aaron Stevens Hi Aaron, Just sent them. Let me know if they don't come through or don't work! –Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 13 Apr, 2016 19:08
DanRussell	Another slightly more complicated way would be to upload it to something like Google Drive or Dropbox from within the VM (using Chrome), and then download it outside the VM. –Dan

Posted in: Starterator → Saving Starterator reports outside of VM

Link to this post \| posted 13 Apr, 2016 18:08
DanRussell	cmageeney Hi Dan, I was wondering if I could be sent the link for the new virtual machine. My entire virtual box is not working and I trying to reinstal everything. I would need the windows version. Thanks Katie Mageeney Hi Katie, Just emailed them to you! Good luck. –Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 11 Apr, 2016 14:04
DanRussell	Steven Felkoski I am a student and would like to be able to use Phamerator on my home computer, could i also get the file? Thanks, Steven Sfel1@umbc.edu Yep, Steven, just emailed them to you. –Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 06 Apr, 2016 20:16
DanRussell	Hi Lee, Looks like that error is my fault! When I updated the consed on the VM, apparently I didn't copy all files from the old consed directory to the appropriate places. This would only affect uses of phred and phrap, which are rarely used, but would definitely be used when adding reads. To fix this on your VM, run the following commands when logged in as seafaculty, entering the password as necessary: `sudo cp /usr/local/genome_OLD/bin/phred /usr/local/genome/bin/` `sudo cp /usr/local/genome_OLD/bin/phrap /usr/local/genome/bin/` `sudo cp /usr/local/genome_OLD/lib/phredpar.dat /usr/local/genome/lib/` This should put the files in the appropriate places and make it work again. You're the first to discover this probably because 1) we barely do any Sanger reads any more and 2) I usually run consed on my Mac rather than within the VM. Sorry, and good catch, –Dan

Link to this post | posted 06 Apr, 2016 20:16

DanRussell

Hi Lee,

Looks like that error is my fault! When I updated the consed on the VM, apparently I didn't copy all files from the old consed directory to the appropriate places. This would only affect uses of phred and phrap, which are rarely used, but would definitely be used when adding reads. To fix this on your VM, run the following commands when logged in as seafaculty, entering the password as necessary:

sudo cp /usr/local/genome_OLD/bin/phred /usr/local/genome/bin/

sudo cp /usr/local/genome_OLD/bin/phrap /usr/local/genome/bin/

sudo cp /usr/local/genome_OLD/lib/phredpar.dat /usr/local/genome/lib/

This should put the files in the appropriate places and make it work again. You're the first to discover this probably because 1) we barely do any Sanger reads any more and 2) I usually run consed on my Mac rather than within the VM.

Sorry, and good catch,
–Dan

Posted in: Consed → Adding Sanger Reads

Link to this post \| posted 04 Apr, 2016 18:41
DanRussell	Hi Greg, Looks like in that paper we mention using ClustalW which has been retired in favor of ClustalOmega to generate the numbers, then NJPlot to draw the trees. –Dan

Posted in: Papers → Pham and Phylogenetic analysis software

Link to this post \| posted 23 Mar, 2016 18:16
DanRussell	ball.1766 I have a student who has Linux on his home computer and would like to download Phamerator. Could you please send me the appropriate file/password that he would need to be able to get it up and running? Thanks, Sarah Hey Sarah, If he's just installing Phamerator on his own Linux system, then he probably just needs this quick guide rather than any pre-made image/file or anything. It's not too tough to get it up and running on Linux. –Dan

Link to this post | posted 23 Mar, 2016 18:16

DanRussell

ball.1766
I have a student who has Linux on his home computer and would like to download Phamerator. Could you please send me the appropriate file/password that he would need to be able to get it up and running?

Thanks,
Sarah

Hey Sarah,

If he's just installing Phamerator on his own Linux system, then he probably just needs this quick guide rather than any pre-made image/file or anything. It's not too tough to get it up and running on Linux.

–Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 07 Mar, 2016 15:25
DanRussell	Hi Greg, If you really want a quick way to check your phages against some others, you could set up a new Phamerator database using the public version of PhamDB we've set up. There's some more info here. I should mention that I would keep all PhamDB databases relatively small for now, fewer than 100 genomes for sure. –Dan Edited 07 Mar, 2016 15:26

Posted in: Phamerator → Analyze our near finished sequence in Phamerator???

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