Link to this post | posted 08 Apr, 2025 22:04
fbaliraine	Thank you, Debbie! I too was inclined to call it NKF given its size and the available HHPred data. Best regards, Fred

Link to this post | posted 08 Apr, 2025 01:42

fbaliraine

DoRead putative gene (54759- 54884 bp) has significant coding potential in both GeneMark_smeg & TB and is part of an operon with the upstream and downstream genes as is common in F1 phages. Its aa sequence is MTYTIGVVAHTKHADQLIHGPQVATVFKANERNTWSWWRHKZ Whereas PhagesDB & NCBI BlASTp yields multiple hits to glycosyltransferase including with phage Madiba gp 100, I note that it is Q4:S441 alignment albeit with 89% coverage, and HHPred shows no significant hits. Would you still call this a glycosyltransferase, or NKF? Fred 213Kb

Link to this post | posted 27 Mar, 2025 18:53
fbaliraine	This helps clarify things! I have left the upstream gene intact (52714-52875 bp) and for the downstream gene (stop 54067 bp), I have changed the start to 52892 bp which is the most annotated start, also called in Che8 gp 108 and has a better RBS score than the auto-called start at 52907 bp. Thank you, Debbie! Fred Edited 27 Mar, 2025 19:02

Link to this post | posted 27 Mar, 2025 07:22

fbaliraine

Phage DoRead draft gene 103 (stop 52875 bp) in the +3 frame has significant coding potential (CP) only in GeneMarkS, and has an 8 bp overlap with the upstream gene which stops at 52721 bp. However, the gene in the +2 frame (stop 54067 bp) and is auto-called to start at 52907 bp has significant CP in both GeneMark_smeg & GeneMark_TB to allow it to start at 52718 bp, with a 4 bp ATGA overlap. Per Guiding Principle 12a, the ribosome is expected to prefer the operon. Keeping draft gene 103 (stop 52875 bp) means that the operon would have to go backwards to start at 52714 bp to make an 8 bp overlap rather than the ATGA overlap (start 52718 bp). So far, only phage Modragons gp104 takes this operon as the start. Several BLASTp results in phagesDB keep the 8 pb overlap start (52714 - 52875 bp) which is found in 69.5% of genes in pham. The start at 52718 which gives the 4 bp overlap is found in 54.2% of genes in pham. I also note that there is a string of operon genes with 1-4 bp overlaps starting from the two upstream genes all the way to the end of the genome (only the start at 52714 bp with an 8 bp overlap would break this pattern). What is your verdict? Change the start to 52718 bp and prefer the operon (meaning deleting the gene which stops at stop 52875 bp) or keep both genes? See attached Edited 27 Mar, 2025 07:50 220Kb

Link to this post | posted 11 Mar, 2025 20:36
fbaliraine	Thank you Debbie for the clarification and congratulations to Krista and the entire Hatfull lab on the new paper in Cell!

Link to this post | posted 11 Mar, 2025 18:24

fbaliraine

Is draft feature 23 of DoRead at position 23627-24265 bp (639 bp long), a minor tail protein? Its aa sequence is: MAYDKQAWQNAPSTETPLSAGALNHMEDGIADAHTLAESKADSEHTHVLADVTDVVASAGEVNVLAGATVSTGELNTLDGVTSNVQTQLDGKAASSHNHSAANVTSGTLDIARIPVGNSGSTVCVGNDSRLSDQRVPVDGSVSSAKIASGSITNTHVSPSAAIAASKMSTGVQASLTKADGSVQKSGTAEGMWMGTTLPGTGTAGVLYVVVPZ Minor tail proteins are typically the 5 big genes (at least1000 bp long) downstream the tape measure…"There are usually not more than 5" (https://genomicsguide.seaphages.org/). We have already identified the other minor tail proteins. We have previously called this NKF, though there are some hits to minor tail proteins in some phages. But I notice a recent deposit in HHPred by Freeman K.G. et al, and this is the is the only significant hit in HHpred, hitting “Minor tail protein; Bacteriophage, tail tip” of Mycobacterium phage Bxb1 with 99.11% probability. Its PDB description at https://www.rcsb.org/structure/9D93 I wanted to cross-check before making the final call. Thanks! Fred Edited 11 Mar, 2025 20:30 119Kb

Link to this post | posted 27 Jan, 2025 17:09
fbaliraine	Hi Debbie, Thank you for your response. I just wish there was a way to zoom in or out of DNA Master or to adjust the text font size, but will settle for what we have. Best regards, Fred Edited 27 Jan, 2025 17:13

Link to this post | posted 25 Jan, 2025 03:31

fbaliraine

The letter font size in DNA Master is quite small, and unlike a pdf or word document, we are unable to zoom in or zoom out. We project the DNA Master file on the white board, but because of the font size, both instructor and students are having trouble seeing the letters on the while screen/board unless we walk up close. I have asked my IT Team here and they tell me there needs to have a way to adjust the font size within the software or to zoom in. We have looked at the preferences but not seen any option to do that. Even if we adjust the font size on the PC, that does not help with DNA Master. Any suggestions? Thanks and Happy annotating! Fred Edited 25 Jan, 2025 03:32

Link to this post | posted 03 Mar, 2024 21:12
fbaliraine	Thank you, Debbie, for helping put this to rest! Fred

Link to this post | posted 02 Mar, 2024 03:30

fbaliraine

We need further clarification about these small genes in subcluster F1: “The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.” Does this principle of calling them in F1 even without coding potential only apply to those “with 4bp overlaps at both ends,” or does it also apply to those with a 4 bp overlap at only one end? For example, FreddyB position 33967 – 34041bp (reverse) in the -2 frame has a potential small gene (75 bp) with a 4bp ATGA overlap with the start of the upstream gene, but there is a gap between it and the downstream gene. This potential gene has a strong RBS score (3.152), though its start is not part of an operon (only its stop is; see attached). Its amino acid sequence is MRMSRSDNASARKLATNTERPTTRZ. It currently has no significant blast hits. Thanks! Fred 119Kb