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

Link to this post | posted 19 Jan, 2024 18:11
debbie	Hi Johann, The header of the fasta file for Franklin22 had a misspelling in it, so it read Frankin22. If you go to Franklin22's page, you can get the info that you need. The header has been corrected, but will not post until sometime later tonight or tomorrow. best, debbie

Link to this post | posted 03 Jan, 2024 12:23
debbie	The most current version of DNA Master is 5.23.6, build 2705, 24 October 2021. Make sure preferences are set correctly, check #6, to make sure that the sftp settings are correct). Then, in preferences, go to "Timed Events' and uncheck the first box. It does not need to check for updates again.

Link to this post | posted 18 Dec, 2023 02:22
debbie	Hi Fred, I would call 28 a holin and 29 a membrane protein. debbie

Link to this post | posted 10 Dec, 2023 01:58
debbie	The 2011 paper describes some repeat sequences in the right arm of The analyzed phages. In annotating phage Feyre, repeats were detected. See attached. 2Kb

Link to this post | posted 08 Dec, 2023 00:12
debbie	The transposase interrupts the N terminus of the immunity repressor (gp 43), and does not appear to be expressed (preliminary testing in the Hatfull lab). Therefore no immunity repressor gene has been called. Some details are in the attached document. 12Kb