Link to this post | posted 29 Apr, 2024 20:39
ejyoon	Thank you for the reply. I just re-ran the HHPred in PECAAN earlier this afternoon. I appreciate your time and help.

Link to this post | posted 26 Apr, 2024 19:29

ejyoon

Thank you for the prompt response. I'm glad that there are people monitoring the forum. I am aware that I can run HHPred manually, and we have done that to collect data for putative function assignment during the semester. We use PECAAN to finalize the annotation and export it to create the required files for QC. We just found the process is easier without having to worry about manually inputting all the data in DNAM for this step. However, if we need to add this information manually into the final DNAM files for QC submission, then we will certainly do that. I was just hoping to avoid that manual work out of convenience.

Link to this post | posted 26 Apr, 2024 16:15

ejyoon

Hello, We are finishing up annotation of a phage (UBSmoodge) and we are finalizing putative function assignments. There are a handful of genes in which HHPred is not updating and providing any results. It keeps queueing repeatedly, and it has been doing so for two days now. Is there anything that I can do to resolve this issue? I just don't know what to do other than keep waiting (and hoping). Thank you for your time and help.

Link to this post | posted 09 Feb, 2021 01:58
ejyoon	Hello, we are annotating Pham 51023 in Figliar, and we can't find a starterator report for this pham. This pham is not an orpham as there are 114 members in this pham. I looked up the pham in phagesDB and it is there, although I do not know how to tell if a pham number has been changed in an update or not. I was hoping to get help with obtaining the starterator report for this pham.

Link to this post | posted 10 Oct, 2020 16:26
ejyoon	Thank you for the reply, Debbie. The UV treatment method is working reasonably well for our lab this semester. Thank you for the suggestion about spotting one culture on the lawn of another. We'll keep that in mind for the future.

Link to this post | posted 21 Sep, 2020 17:13

ejyoon

Hello, We are seeking some advice about the best protocols or practices to induce and "force" bacteriophages to switch from a lysogenic cycle to a lytic cycle for the purification and amplification steps of phage discovery. We are using Gordonia rubripertincta for our host organism this fall. We are contemplating exposing the infected bacterial cells (right after being plated with top agar) to UV radiation for very short time periods. We recently tried growing the infected bacteria at a higher temperature than their optimal to force the phages out of lysogeny; however, that method did not work. Any suggestions and insight are appreciated. Thank you for your time. Edited 21 Sep, 2020 17:14

Link to this post | posted 23 May, 2019 05:03

ejyoon

We saw some smearing in our gels. This was our first year so we did not know what to expect and believed the smearing to be due to human or equipment error (and we are not ruling that out). I've attached an image of a gel that shows faint smearing throughout the cut lanes (not much uncut DNA present in the first lane unfortunately). Fortunately, we were able to get sequencing back for our phages (the attached gel image is from one of those sequenced phages). 257Kb