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Recent Activity
Dan Russell posted in Congrats to Steve Caruso and Beth Wilkes — 2025 ASM Outstanding Instructor Award, Honorable Mention
ACMPhageHunters posted in Clarification Question About HNH Endonuclease Function Determination in view of hits to the Ref Sequences
cdshaffer posted in Clarification Question About HNH Endonuclease Function Determination in view of hits to the Ref Sequences
All posts created by scaruso
| Link to this post | posted 17 Mar, 2021 23:12 | |
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I was just QC'ing TunaTartare, a BK1, and came across this thread as it was growing. I was about to chime in that TT has the CCCAAAT, but Chris just beat me to it. And with a lot more as well! Steve |
Posted in: Frameshifts and Introns → No frameshift in cluster BK1?
| Link to this post | posted 25 Sep, 2020 00:24 | |
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Chris, Excellent. And thank you for the very clear directions with sample. Worked perfectly. Steve |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 24 Sep, 2020 20:07 | |
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Thank you, Chris. I will give that a try! Steve |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 24 Sep, 2020 12:02 | |
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Thank you. I am going to advise they use Aragorn for now and revisit with tRNAScan-SE later in the semester, unless you suggest otherwise. Steve |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 24 Sep, 2020 10:22 | |
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Hello, Several students have reported to me that they are not getting results from tRNAScan-SE over the last week. So I just tried it, and let it run all night and had the same experience. It just stalled while working on a cluster BE, which has lots, and lots of tRNAs. Does anyone know something about tRNAScan-SE? Thanks, Steve |
Posted in: tRNAs → tRNAScan-SE Down-ish?
| Link to this post | posted 09 Sep, 2020 01:47 | |
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I need a way to more easily see their screens. Steve |
Posted in: DNA Master → Novel Student Issue
| Link to this post | posted 09 Sep, 2020 01:47 | |
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Darn it. I knew that would be the answer. Steve |
Posted in: DNA Master → Novel Student Issue
| Link to this post | posted 09 Sep, 2020 01:38 | |
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I am getting my students started using DNAM, online, of course, and one has run into a novel problem. I am sure it's something simple, but I sure can't figure out how they are getting this result. First they are running through a practice genome I use for training, and this student is getting a RBS results window that looks weird. I did ask if he is running DNAM as an administrator and if it had been updated. Anyone ever see this version of the RBS screen? Note that the column headers are wrong, no Z score, not final score. Thanks! Steve |
233KbPosted in: DNA Master → Novel Student Issue
| Link to this post | posted 04 Sep, 2020 14:12 | |
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Thanks, Debbie. Sorry to add to your plate. Never rains, but it pours. Steve |
Posted in: DNA Master → Blast error
| Link to this post | posted 04 Sep, 2020 12:30 | |
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This is bad timing since I have 120 students blasting genes starting this weekend. Just to confirm, I checked it this morning on another computer and on the UMBC virtual desktop and got the same result. So it looks like either NCBI is having a problem or the connection between DNAM and NCBI has one. I did check NCBI online, and it is working, so it isn't the main BLAST system. Steve |
Posted in: DNA Master → Blast error