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Link to this post \| posted 03 Sep, 2025 23:36
debbie	fixed!

Posted in: Bioinformatic Tools and Analyses → Genome length listed as unknown for phage PestoPenguin on PhagesDB

Link to this post \| posted 02 Sep, 2025 13:23
debbie	Kissaou, The power of comparative genomics will aid in this quest to see if it is plausible that a gene is present in this area. If there an open reading frame that looks plausible. you can blast n and blast p the area. if this area is highly conserved, what are the possible explanations? If it is not conserved, what does that tell you. Check out the dates of the genomes that have this sequence. What have they called. What is the evidence on which they made their calls. That data is all present in the tools that you have access to. Lots of information, tricky decision. let us know what you find out. debbie

Link to this post | posted 02 Sep, 2025 13:23

debbie

Kissaou,
The power of comparative genomics will aid in this quest to see if it is plausible that a gene is present in this area.
If there an open reading frame that looks plausible. you can blast n and blast p the area.
if this area is highly conserved, what are the possible explanations? If it is not conserved, what does that tell you. Check out the dates of the genomes that have this sequence. What have they called. What is the evidence on which they made their calls. That data is all present in the tools that you have access to. Lots of information, tricky decision.
let us know what you find out.
debbie

Posted in: Functional Annotation → a gene in this gap?

Link to this post \| posted 02 Sep, 2025 13:18
debbie	Kissaou from Austin Community college wrote: I am kissaou , and I am making this post regarind Mycobacterium phage "Teodoridan" Cluster A1 we completed the annotation, but I am a little it not happy about the 311 bp between gene 2 and gene 3. Any idea? Looking at DNA master frames, it is possible to inser a gene between Start 1474bp - stop 1665bp. However, looking at glimmer and genemarks, there is not a reall coding potential. What everybody else think? Thanks Kissaou

Link to this post | posted 02 Sep, 2025 13:18

debbie

Kissaou from Austin Community college wrote:
I am kissaou , and I am making this post regarind Mycobacterium phage "Teodoridan" Cluster A1
we completed the annotation, but I am a little it not happy about the 311 bp between gene 2 and gene 3.
Any idea? Looking at DNA master frames, it is possible to inser a gene between Start 1474bp - stop 1665bp. However, looking at glimmer and genemarks, there is not a reall coding potential.
What everybody else think?
Thanks
Kissaou

Posted in: Functional Annotation → a gene in this gap?

Link to this post \| posted 28 Aug, 2025 14:24
debbie	Ombeline, Hi. I don't have time to troubleshoot, but I will make your profiles for you. Would you send me well labeled files and I will get them back to you? Best, debbie

Posted in: DNA Master → Can´t make profile

Link to this post \| posted 14 Aug, 2025 17:29
debbie	Rick, Very nice. Also a very fun area to think about. Cluster FK are not the only ones to have these. Cluster Bs, and Os also. Any categorization of these would be helpful! debbie

Posted in: Cluster FK Annotation Tips → Huge Region with Puative Intergenic Regulatory Regions

Link to this post \| posted 11 Aug, 2025 15:16
debbie	Hi Randy, This is going to take a bit of time to check. And i don't have that time, so maybe I can provide enough info' to get you started. Historically, it was thought that all sipho have TACS, canonically directly upstream of the tape measure. There is now reports that the genes are present, and do not have to be beside each other. And that not all sipho have TACs. There is also evidence that the 4 nucleotide sequence of XXXY can constitute a slippage (if they are in the 'right spacing' of the reading frames). That is part of the evaluation that can occur. Having the numerous cluster members to compare will also be informative. I don't know what you meant about a second slippage site. You are correct to look more closely. debbie

Link to this post | posted 11 Aug, 2025 15:16

debbie

Hi Randy,
This is going to take a bit of time to check. And i don't have that time, so maybe I can provide enough info' to get you started.
Historically, it was thought that all sipho have TACS, canonically directly upstream of the tape measure. There is now reports that the genes are present, and do not have to be beside each other. And that not all sipho have TACs. There is also evidence that the 4 nucleotide sequence of XXXY can constitute a slippage (if they are in the 'right spacing' of the reading frames). That is part of the evaluation that can occur. Having the numerous cluster members to compare will also be informative.
I don't know what you meant about a second slippage site.
You are correct to look more closely.
debbie

Posted in: Frameshifts and Introns → TAC frameshifts in CF

Link to this post \| posted 29 Jul, 2025 17:26
debbie	Thanks Chris!

Posted in: Cluster AS Annotation Tips → deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.

Link to this post \| posted 28 Jul, 2025 20:36
debbie	I checked this out and realized I needed to gain some basic (very basic) biochem) to my understanding: Nucleoside Deoxyribosyltransferase (NDT): Function: NDT transfers deoxyribose from one nucleoside to another, effectively swapping bases. Deoxycytidylate Deaminase (DCTD): Function: DCTD specifically deaminates dCMP to dUMP, removing an amine group. My question is what are the residues/domains that could help to differentiate these? Maybe, my question is how do you recognize a deaminase domain vs a transferase domain? just maybe… debbie

Link to this post | posted 28 Jul, 2025 20:36

debbie

I checked this out and realized I needed to gain some basic (very basic) biochem) to my understanding:
Nucleoside Deoxyribosyltransferase (NDT):
Function: NDT transfers deoxyribose from one nucleoside to another, effectively swapping bases.

Deoxycytidylate Deaminase (DCTD):
Function: DCTD specifically deaminates dCMP to dUMP, removing an amine group.

My question is what are the residues/domains that could help to differentiate these?

Maybe, my question is how do you recognize a deaminase domain vs a transferase domain? just maybe…

debbie

Posted in: Cluster AS Annotation Tips → deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.

Link to this post \| posted 09 Jul, 2025 13:53
debbie	Julie, Hi. I have no data to help with this one. Best, debbie

Posted in: Lysogeny/Immunity → Inducing phages from lysogeny to lytic cycle

Link to this post \| posted 25 Jun, 2025 14:39
debbie	Ping, I think a titer of any number is sufficient if you have purified the bacteria such that residual phage from somewhere outside of the cell is removed. I would not evaluate this is a vacuum. are the cells homo-immune to that phage infection. Build the evidence and then see what it tells you. We do not have empirical numbers, but you can collect that data. (And then we would for each phage.) Best, debbie

Link to this post | posted 25 Jun, 2025 14:39

debbie

Ping,
I think a titer of any number is sufficient if you have purified the bacteria such that residual phage from somewhere outside of the cell is removed.

I would not evaluate this is a vacuum. are the cells homo-immune to that phage infection. Build the evidence and then see what it tells you.

We do not have empirical numbers, but you can collect that data. (And then we would for each phage.)

Best,
debbie

Posted in: Lysogeny/Immunity → Liquid phage release assay

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All posts created by debbie