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

Link to this post | posted 29 Jan, 2024 03:57

debbie

Hi Chris, I went looking for the tRNA using Aragorn. It did not call it. I should have done my due diligence! Holly - check out this paper for consideration: Bacteriophage tRNA-dependent lysogeny: requirement of phage-encoded tRNA genes for establishment of lysogeny https://pubmed.ncbi.nlm.nih.gov/38236026/ I am not suggesting that your genome has a legit tRNA, but this paper describes the first case that we have published where a tRNA is found in the reverse direction while a protein coding gene is in the forward direction. Great classroom conversation! debbie

Link to this post | posted 26 Jan, 2024 20:17

debbie

Hi Holly, I don't believe it skipped a number, but rather called something that could not be demonstrated in phamerator. But i don't know what that is. It is not uncommon that numbers of genes don't match between your annotation and what is posted on phamerator. what is posted on phamerator is also what 'feeds' what is posted on phagesDB, so they will indeed match. Hence, I request that one never uses gene numbers (but rather use stops) to identify what gene you are working on. i hope that helps, debbie