SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 15 Sep, 2016 20:41
DanRussell	Shallee Page Any Mac people who can help me with some basic WINE setup? Shallee pages@franklinpierce.edu Hey Shallee, Don't know if you're heading for DNA Master in general, but there's a forum topic here for that. There's also a new document about DNA Master on Mac. (The XQuartz part will probably be relevant to any WINE program, but the other stuff is DNA Master-specific.) –Dan Edited 19 Sep, 2016 13:31

Link to this post | posted 15 Sep, 2016 20:41

Shallee Page
Any Mac people who can help me with some basic WINE setup?
Shallee
pages@franklinpierce.edu

Hey Shallee,

Don't know if you're heading for DNA Master in general, but there's a forum topic here for that. There's also a new document about DNA Master on Mac. (The XQuartz part will probably be relevant to any WINE program, but the other stuff is DNA Master-specific.)

–Dan

Edited 19 Sep, 2016 13:31

Posted in: SEA-PHAGES Virtual Machine → WINE

Link to this post \| posted 13 Sep, 2016 19:18
DanRussell	Hi all, Attached to this message (and linked here) is a document describing the project. –Dan Edited 13 Sep, 2016 19:18 37Kb

Posted in: Xeno Project → Basic Xeno Project Information

Link to this post \| posted 13 Sep, 2016 19:14
DanRussell	Hi all, Attached to this message (and linked here) is a document describing the project. –Dan 34Kb

Posted in: Host-Range Project → Basic Host Range Project Information

Link to this post \| posted 13 Sep, 2016 18:41
DanRussell	This forum is primarily meant to be a container for all the different sub-forums that will contain information about annotating specific clusters and subclusters of phages. While everyone was trained in general to do phage annotations, there are certain things that might be of particular interest given the particular cluster you end up annotating. Cluster M? It'd be good to know about tRNAs! Cluster G? Look out for mobile elements! If you have questions about a particular phage/group, please ask them in the appropriate sub-forum. Good luck! –Dan

Link to this post | posted 13 Sep, 2016 18:41

DanRussell

This forum is primarily meant to be a container for all the different sub-forums that will contain information about annotating specific clusters and subclusters of phages. While everyone was trained in general to do phage annotations, there are certain things that might be of particular interest given the particular cluster you end up annotating. Cluster M? It'd be good to know about tRNAs! Cluster G? Look out for mobile elements!

If you have questions about a particular phage/group, please ask them in the appropriate sub-forum. Good luck!

–Dan

Posted in: Cluster-Specific Annotation Tips → Using This Forum

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

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

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

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