Link to this post | posted 07 Feb, 2024 01:10

debbie

Hi all, If you are looking how to instal PDM utils on a M1 mac, you can follow this: On a series of MacBook Pro computers, including most recently an M1 mac, I have only ever done native installs of pdm_utils. The hardest part for me is MySQL – use an installer for 8.0.18 or later (earlier versions had funky bugs related to cascaded deletes!). Choose “Legacy Password” when prompted, and you’ll be forced to choose an 8-character or longer password (no more ‘phage’). Make sure you add mysql to the $PATH (export PATH=’/usr/local/mysql/bin:$PATH’) in your ~/.zshrc file. Other than that, if you use some flavor of conda to manage the third-party dependencies (Aragorn, trnascan-se, mmseqs2, blast) pdm_utils should be just fine. –Christian Gauthier Edited 07 Feb, 2024 01:21

Link to this post | posted 06 Feb, 2024 02:10

debbie

Hi Adam, I know very little about Streptomyces phages annotations. When I first looked at this, I most wanted to respect coding potential. Tonight, I had to ask - after your most recent questions - how many BD phages are there. Looks like there are 43 members in BD, with 11 in subcluster BD2. And additional phages in the rest of the BD subcluster. My impression is that the right arms of BD phages are filled with small genes and lots of HGT. Because of the overlap, I expected to see lots of hits to the c terminus of this overlapping gene. But if you blastn 44271- 43849, you can see what this looks like athere are 2 genes in the region. My take, with the short amount of time I have looked at this, is that there is no clear answer here. If you choose the longer overlap, please be sure to include your justification when you submit. There is definitely more digging to do. And no, this won't get answered until you look at all the data, don't leave out the functional investigation as you continue to consider this. debbie

Link to this post | posted 05 Feb, 2024 18:16
debbie	Hi all, For the past week or so the tRNA Aragorn site is not responding. We are investigating. I'll keep you posted. debbie Feb. 13, 2024 Argorn is back up at a new location The new site is running Aragorn 1.2.41 and can be found here. http://www.trna.se/ARAGORN/ Edited 13 Feb, 2024 16:17

Link to this post | posted 02 Feb, 2024 15:02

debbie

Adam, Next time, please use coordinates. I just looked too quickly, my apologies. I would call the big overlap. This is a great opportunity to imagine how a toxin/antitoxin pair would work. and that is saying that i am not sure it is even a toxin/antitoxin pair. Another key point, you aren't done with your positional annotation until you have looked at the functional annotation. You can convince yourself that the gene and the start are the right calls, but investigating the functional call may show you you are wrong because you are missing a needed domain or the opposite - there is no functional information the helps. As for the picture that you sent, the dissimilar nucleotide sequence in the bottom genome negates inferring anything about what genes to call in your genome without further inspections. do you use the multiple protein seqeuece alignments from phagesDB/phamerator? In this case, you may want to call a toxin, but can you identify an anti-toxin? so many good questions! debbie

Link to this post | posted 02 Feb, 2024 13:17

debbie

Hi Adam, This is not a gap-filling exercise. There is great coding potential. If I am at the correct gene (you didn't provide coordinates), there is a 31 base overlap between the gene that starts at 44145 and the next one that ends at 44114. Not that troublesome in this context. Just as important is that there are interesting hits to the gene that ends at 44114. More investigation is needed but I would want to know if I can make a 'toxin' or a DNA binding functional assignment. Edited 02 Feb, 2024 13:20

Link to this post | posted 01 Feb, 2024 17:11
debbie	Hi Jacob, 1. Please send me the file from one of the computers. (not from your computer.) 2. What version of Windows are you using? My guess is that those computers are missing a driver or help file. 3. Check the DNA Master folder, where the drivers are stored. Check to see if the files listed match yours.) debbie

Link to this post | posted 01 Feb, 2024 15:11
debbie	Hi Arturo, the answer to this one is found here: https://seaphages.org/forums/topic/5207/ Please don't call it based on the data that is showing up at this point. Best, debbie

Link to this post | posted 31 Jan, 2024 02:04
debbie	afreise The approved function list still lists the old evidence requirements (TmHmm, TOPCONS) for membrane proteins - could this be updated? https://docs.google.com/spreadsheets/d/e/2PACX-1vToasuRfxx_yfLa9ECFN4_6okwNI_5AJGWZ3NCy53Gz0QfoNrhAQ48HnBuSD1hsrY0zUTTn6EP3MGK_/pubhtml?gid=0&single=true Not anymore. Approved Function now states to use DeepTMHMM.

Link to this post | posted 31 Jan, 2024 02:00
debbie	Kurt, only DeepTMHMM is used. Please see the January Faculty Meeting forum post for more information. https://seaphages.org/forums/topic/5612/ debbie

Link to this post | posted 30 Jan, 2024 21:25
debbie	Jacob, Hmmm. I am not sure. Is it a color thing? Go to preferences and change the colors and see if that fixes it. Are there "names" in the feature table of the DNA Master file? (that is where the numbers come from.) debbie