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

Link to this post | posted 24 Jan, 2024 00:49

debbie

Amanda, I see no canonical slippage in RomansRevenge either. The real trick is that I could believe that the "T" portion of a tail assembly chaperone is present, but there is really no way to call it without a useful start codon. debbie BTW The gene that precedes the tail assembly chaperones has hits to minor capsid, HK97_gp 10 and minor tail protein. While I am confident that this protein is structural, it is not clear whether it is part of the head or the tail, please call it Hypothetical Protein.

Link to this post | posted 20 Jan, 2024 23:28

debbie

Fred, i haven't looked at this specifically, but the cluster F1s are notorious for having MANY tiny genes that have the 1-4bp overlap with the preceding and next genes. So there are calls 'without' coding potential. As you have mentioned, it just makes sense to call them. Please remember that coding potential is not the end-all. The math (and remember that coding potential is an interpolated markov model - a mathematical calculation - that may or may not hold true when applied to small genes. debbie

Link to this post | posted 20 Jan, 2024 01:09
debbie	Others can give more specifics, but we have found TopCons to be confusing. It runs 5 (ish) different programs that contradict each other. DeepTMHMM has shown to be most reliable. results from DeepTmHmm are incorporated in phamerator. debbie