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

Link to this post | posted 08 Dec, 2023 00:06
debbie	The immunity repressor in Feyre (gp 43) is interrupted by the insertion of the transposase. Preliminary testing shows that Feyre does not make a lysogen (and the immunity repressor is not working).

Link to this post | posted 01 Dec, 2023 04:59

debbie

More papers about cluster K phages: Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4 https://pubmed.ncbi.nlm.nih.gov/30948168/ A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells https://pubmed.ncbi.nlm.nih.gov/17083467/ Mycobacteriophage TM4: genome structure and gene expression https://pubmed.ncbi.nlm.nih.gov/10645443/ Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn https://pubmed.ncbi.nlm.nih.gov/29217790/ Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007. https://pubmed.ncbi.nlm.nih.gov/29122862/ Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557439/ Edited 01 Dec, 2023 05:05