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

Link to this post | posted 16 Feb, 2024 22:09

fbaliraine

Hi Debbie, Thank you for your insights. I still do not have a strong justification for keeping this gene, so I will go ahead and delete it. There is no coding potential, the region is left unfilled in D29 & L5, and I note that whereas nucleotide sequence is conserved across many genomes, only the above mentioned few call it. If a researcher wants to investigate that “gene” which has been called in the above-mentioned phages, it will be interesting if they get a gene product and possibly a function, in which case we would have stronger support for calling a gene in this region in future annotations. Thanks again! Fred

Link to this post | posted 15 Feb, 2024 05:05

fbaliraine

We have not seen any coding potential whatsoever for subcluster A4 pham 4236 in GeneMark_S, smeg or TB for the very last Gimmer-autocalled reverse “gene” in Alberto7 (51374 to 51204 bp) and Lunsford (51030 to 50860 bp). We note that this “gene” (MTSLTASCSVVLDNSTADIANRFGNPHASGFETAQRTGTLRTSRINPALDIAQSISZ) comes after a very large gap (710 bp gap, with no coding potential in the gap) from the preceding gene. We do not see any significant HHPred hits (probabilities range from 20.07-63.7%). We however see significant BLASTp hits in phagesDB with 17 previously annotated genes, with 100% homology (see attached). To find out some possible justification for this pham, in case at least one member of the has significant coding potential, we decided to check for coding potential in all the draft and non-draft phage “genes” that match the above “genes” in phagesDB. We have found no evidence of coding potential for this gene in any of the 21 current pham members: Tinybot_89 [51068 to 50898 (Reverse)]; Taquarus_89 [51040 to 50870 (Reverse)]; Scamp_90 [51039 to 50869 (Reverse)]; Ohfah_91 [51078 to 50908 (Reverse)]; NotAPhaseMom_89 [51042 to 50872 (Reverse)]; Maxo_92 [51044 to 50874 (Reverse)]; Maverick_91 [51038 to 50868 (Reverse)]; Lunsford_draft_86 [51030 to 50860 (Reverse)]; LochMonster_91 [51274 to 51104 (Reverse)]; Lemur_89 [51034 to 50864 (Reverse)]; Koreni_90 [50721 to 50551 (Reverse)]; Jaykayelowell_86 [51031 to 50861 (Reverse)]; Houdini22_89 [51042 to 50872 (Reverse)]; Deano_86 [51045 to 50875 (Reverse)]; ChampagnePapi_92 [51477 to 51307 (Reverse)]; Cerulean_92 [51475 to 51305 (Reverse)]; CentreCat_90 [51078 to 50908 (Reverse)]; Bombshell_91 [51038 to 50868 (Reverse)]; Alberto7_Draft_85 [51374 to 51204 (Reverse)]; LappelDuVide_Draft_85 [51037 to 50867 (Reverse)]. We are now of the view that apparently, the only reason this gene was called was because it was autocalled by Glimmer. I am strongly of the view that this gene should be deleted, but because it has been previously called in number of phages, I do not want to kill it without giving it an appellant opportunity. Any strong defense in favor of keeping it? Thanks! Fred Edited 15 Feb, 2024 05:06 101Kb