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Debbie Jacobs-Sera posted in Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage
All posts created by DanRussell
| Link to this post | posted 16 Nov, 2016 15:08 | |
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Hi all, If you're experiencing recent problems with DNA Master, it's probably because of the update of NCBI to use secure connections. See the blog post and forum below, but the gist of it is that DNA Master was updated on Nov 15, 2016 to be able to handle this, so if you haven't updated your DNA Master since then, please do so! http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ http://seaphages.org/forums/topic/214/ –Dan |
Posted in: DNA Master → Glimmer Failure on Auto Annotation
| Link to this post | posted 16 Nov, 2016 15:06 | |
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New as of November 15, 2016 Some very important changes have been made to DNA Master to accommodate NCBI's new secure https protocols. Versions of DNA Master from before this date will not be able to connect to NCBI and thus will not be able to auto-annotate genomes or run BLAST. Updating your DNA Master will allow you to be able to use NCBI's new protocols. See this blog post for more information. http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ –Dan |
Posted in: DNA Master → Important DNA Master Update
| Link to this post | posted 15 Sep, 2016 20:41 | |
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Shallee Page 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 |
Posted in: SEA-PHAGES Virtual Machine → WINE
| Link to this post | posted 13 Sep, 2016 19:18 | |
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Hi all, Attached to this message (and linked here) is a document describing the project. –Dan |
37KbPosted in: Xeno Project → Basic Xeno Project Information
| 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