Link to this post | posted 19 May, 2022 17:02
stpage	They never emailed me back but we seem to be ok if we are rather gentle with HHPRED. Specifically, don't: -copy over a previous input and resubmit under a new ID -launch multiple HHPRed searches simultaneously under the same browser Sometimes, it seems to help to erase the previous job before entering a new job and launching. It's nice that I can still find inventive ways to break things.

Link to this post | posted 11 May, 2022 12:41

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Um, has anyone ever gotten kicked out of HHPRED? My student and I were launching multiple HHPRED jobs (3-4) in multiple tabs and now both of our IPs have been blocked apparently. I can search on a different laptop but when we search on those two laptops, we get "ERROR!". We tried to clear cookies and restart and nope, HHPRED still throws the error, so I think it might be IP-based. I get the error whether I am logged into an HHPRED account or not. If we are the first, um, well, word to the wise. Edited 11 May, 2022 12:43

Link to this post | posted 14 Mar, 2022 14:25
stpage	Hi, we had this discussion when we annotated MarioKart a little over a year ago. I am not sure that there is not a frameshift but just felt like there wasn't enough evidence to call it. Nhagos and Sours have 4 Gs around the end of gene 21 that is the region identified as the slippery sequence. Does yours have Pham 113375 or 115039? It might be worth tracking it by Pham rather than by cluster.

Link to this post | posted 15 Nov, 2021 17:17
stpage	fogartym1 Thanks Vic! We will try it out and report back on how it goes. Marie Hi, did you ever have any luck with this? I have a student who has apparently lost their phage that they isolated a couple of weeks ago. We'd like to take his old plaques and PB and amplify them back up. Thanks.

Link to this post | posted 27 Oct, 2021 23:34
stpage	Thanks, Vic. That is helpful. We were losing some DNA and weren't sure if we were getting capsid denaturation from the proteinase K. Different protocols seem to have wildly different proteinase K conditions.

Link to this post | posted 27 Oct, 2021 19:27

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Hi, the phage discovery has RNase/DNase/ProteinaseK treatment followed by CleanupResin (guanidinium thiocyanate) to denature the capsid. Some protocols seem to use proteinaseK to denature the capsid. (https://www.mdpi.com/2409-9279/1/3/27/pdf-vor) and some seem intermediate (https://pubmed.ncbi.nlm.nih.gov/29417429/). Is it very phage dependent? With new hosts do we need to optimize the proteinaseK treatment??

Link to this post | posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Link to this post | posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Link to this post | posted 19 Feb, 2021 19:16
stpage	stpage Thanks, Chris. That was pretty peppy response for a Friday afternoon….@! FIrefox worked, thanks.

Link to this post | posted 19 Feb, 2021 19:12
stpage	Thanks, Chris. That was pretty peppy response for a Friday afternoon….@!