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Recent Activity
All posts created by scaruso
| Link to this post | posted 04 Aug, 2020 14:47 | |
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Chris, Just installed the new version of the VM for genome checking and I'm running into two problems that might be related. I'm having trouble updating Phamerator the first time and Starterator 1.2 won't run. It just closes. I assume that's because the Phamerator DB isn't getting set up? Does that make sense? Steve |
Posted in: Starterator → Release of Starterator version 1.2
| Link to this post | posted 11 Mar, 2020 22:44 | |
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As so many of us are no doubt experiencing, UMBC has just moved to online learning for at least the time being. Perhaps for the entire semester. That is one thing (though not great) for the in silico part of the class. But I was asked today by my dean about how we can make a three-week version of the in situ lab I teach in the Summer on line. Of course, I am already wondering what might happen if this extends into the Fall. Many of you are much, much brighter than I am. I am hoping that you have some exceptional ideas that I can steal. So? Has anyone thought of how they might deal with that if it comes to it? Steve |
Posted in: General Message Board → Converting to Online?
| Link to this post | posted 11 Mar, 2020 22:40 | |
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I was asked by my dean about how we can make a three-week version of the in situ lab I teach in the Summer on line. That's not helpful, I know, but I was just about to post that when I saw this. :< Anyway, to your question. We created a series of short videos demonstrating some of the simple tools like making Gepard plots, calculating ANI and OrthoANI, and gene content; and some more complex ones like making phylogenetic trees, using Splitstree (has that been streamlined yet?), and SNP analysis. We give them some tools and turn them loose along with some advice on how to ask questions. But that's something that could be done quickly and at a distance. Steve |
| Link to this post | posted 09 Mar, 2020 13:00 | |
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I appreciate this conversation, by the way, and the new notes on the approved functions list. There was a lot written on lysin A structure (in Mycos) but not the limit on using the designation. So it's good to get the clarification. Steve |
Posted in: Cluster BD Annotation Tips → lysin A
| Link to this post | posted 11 Dec, 2019 01:44 | |
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Been using it, and it's great! Steve |
Posted in: Starterator → Release of Starterator version 1.2
| Link to this post | posted 01 Dec, 2019 20:21 | |
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If I can make sure I am perfectly clear? This is generalizable, correct? If we see GTGATG or ATGATG, go with the second as a rule, and not just in clusters O, J, and M. I presume it is also true with TTGATG? Steve |
Posted in: Choosing Start Sites → GTGA overlaps
| Link to this post | posted 01 Oct, 2019 15:34 | |
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Hello, I hesitate to ask this question because I don't want to imply impatience. But I want to know what to tell students who are asking me questions. So, here goes. How often are phages entries checked in to PhagesDB? I am hoping to give students some sort of estimate, if possible, and prevent some of the double entries I know you get. Thanks! Steve |
Posted in: General Message Board → Phages DB Entries
| Link to this post | posted 18 Aug, 2019 20:03 | |
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I see you added Topcons now, too. Cool! Steve |
Posted in: PECAAN → New Features in PECAAN
| Link to this post | posted 12 Aug, 2019 18:34 | |
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Welkin, The thing that worries us about both this and Nehal 03 was that it looked a lot like we were seeing just the DNA binding part of a gene, like with the many anti-toxin hits we get that are really just HTH-domains. But it was similar enough to the previous call to merit a look. Thanks! Steve |
| Link to this post | posted 12 Aug, 2019 00:47 | |
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Hello all, I think I might have the 'terminase, small subunit' in the BE2 IchabodCrane, which hasn't yet been identified. It looks very similar to gp3 from NEHalo in terms of coverage and the coiled-coils hits using PCOILS described in the forum post: https://seaphages.org/forums/topic/4736/. IchabodCrane_gp121 MKECPICGKDKELDEFGRQITNPSKFYKWCRDCRLSMARRKKNNFDEGRALRSKTVQLRRLTDAQVTEVRLLAEWNTPYTEIAQQYGVSATTISKVVNRGYANVY HHPred https://toolkit.tuebingen.mpg.de/#/jobs/Ichabod_g121 PCOILS https://toolkit.tuebingen.mpg.de/#/jobs/ICH121 For reference, NEHalo gp3 in HHPred and PCOILS: HHPred https://toolkit.tuebingen.mpg.de/#/jobs/NEHALO3b PCOILS https://toolkit.tuebingen.mpg.de/#/jobs/NEHALO3 Let me know what you think. Thanks! Steve |