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Recent Activity
All posts created by DanRussell
Link to this post | posted 13 Sep, 2016 19:14 | |
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Hi all, Attached to this message (and linked here) is a document describing the project. –Dan |
Posted in: Host-Range Project → Basic Host Range Project Information
Link to this post | posted 13 Sep, 2016 18:41 | |
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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 | |
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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 | |
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Matt Benczkowski 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 | |
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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 | |
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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 | |
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cmageeney 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 | |
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Steven Felkoski 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 | |
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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:
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 | |
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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