SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 20 Feb, 2025 21:29
debbie	Hi all, Here are my 2 cents. See attached. debbie 145Kb

Posted in: Cluster AS Annotation Tips → Tail Assembly Chaperone- Translational Frameshift

Link to this post \| posted 20 Feb, 2025 17:47
debbie	Hi Nikki, You have done what I would have done. It is, I think, a Windows error. Have you closed and re-opened DNA Master? You may have to re-start Windows. if you send me the file, i can make it for you. debbie

Posted in: DNA Master → Can´t make profile

Link to this post \| posted 20 Feb, 2025 15:18
debbie	Hi Jennifer, Have you done any EMs of SwissCheezer? Or looked at EMs of phages of this cluster? I can finish the answer, but I would rather you look there first and let me know what you think. Thanks, debbie

Posted in: Cluster EK Annotation Tips → Hypothetical Protein or Tape Measure?

Link to this post \| posted 19 Feb, 2025 20:03
debbie	Arturo, Hi. i don't think that the lysis cassette is a reflection of virion morphology. Many phages in our collections have 2 gene that do the function(s) of the endolysins. the mycobacteriophage papers on endolysins are helpful to determine the domains of the endolysins. the exact structure of the cell well is not as clearly understood in the Microbacterium, so we have not seen the gene that corresponds to lysin B. But we have seen the lysin A (endolysin) function to be across 2 separate genes, just like this. Call you genes endolysin, but then list the prominent domain that it is hitting. https://pubmed.ncbi.nlm.nih.gov/22470512/ debie

Link to this post | posted 19 Feb, 2025 20:03

debbie

Arturo,
Hi. i don't think that the lysis cassette is a reflection of virion morphology. Many phages in our collections have 2 gene that do the function(s) of the endolysins. the mycobacteriophage papers on endolysins are helpful to determine the domains of the endolysins. the exact structure of the cell well is not as clearly understood in the Microbacterium, so we have not seen the gene that corresponds to lysin B. But we have seen the lysin A (endolysin) function to be across 2 separate genes, just like this. Call you genes endolysin, but then list the prominent domain that it is hitting.
https://pubmed.ncbi.nlm.nih.gov/22470512/
debie

Posted in: Functional Annotation → Two endolysins?

Link to this post \| posted 12 Feb, 2025 23:55
debbie	Nope. Are you experimentally determining them? Are they like other published AttPs? It is a good question to ask. For now, it can be kept in the DNA Master files the annotation notes that you submit on phagesDB. debbie

Posted in: Annotation → annotating attP site

Link to this post \| posted 11 Feb, 2025 19:03
debbie	Olga, The answer is not about accuracy. Rather more about convention and acceptable practice. It is a historical decision between our program and NCBI. It was agreed that Hypothetical Protein was an acceptable term that both parties (SEA-PHAGES and NCBI) was willing to propagate without changing. So while unknown function could be used, it is not. the programs that categorize this stuff needs continuity to function properly, leading us to adopt Hypothetical Protein as a best choice. debbie

Link to this post | posted 11 Feb, 2025 19:03

debbie

Olga,
The answer is not about accuracy. Rather more about convention and acceptable practice.
It is a historical decision between our program and NCBI. It was agreed that Hypothetical Protein was an acceptable term that both parties (SEA-PHAGES and NCBI) was willing to propagate without changing. So while unknown function could be used, it is not. the programs that categorize this stuff needs continuity to function properly, leading us to adopt Hypothetical Protein as a best choice.
debbie

Posted in: Functional Annotation → hypothetical or NKF

Link to this post \| posted 11 Feb, 2025 17:38
debbie	Hi Olga, Technically there is no difference. However, "Hypothetical Protein" is the only acceptable choice. debbie

Posted in: Functional Annotation → hypothetical or NKF

Link to this post \| posted 08 Feb, 2025 15:39
debbie	Hi Kristen, I will send you to the literature for this. When Dr. Lawrence adopted this method of SD determinations, he used the work of Dennis Kibler and Sam Karlin. I was under the impression that the spacer distance was between the end of the Shine DalGarno sequence and the start. Since SD sequence rarely match the lambda sequence, and the non-perfect matches have weighting schemes, i don't know how to count. the manual has a Kibler reference and here is a Karlin reference. Go to the preference settings of DNA master and note that we have picked Kibler 6 and Karlin medium (quite arbitrarily). But the matrixes provided are quite involved. Other questions: The Z score uses the final score. But note that both numbers reflect similar relationships. "Karlin Medium Shine-Dalgarno spacer matrix in the local settings of DNA Master" - the DNA Master setting (if you are using the most updated DNA Master are Karlin-Medium scores (unless you change your settings in the preferences. Remember, both Kibler and Karlin are applying math to a 'best fit' situation. some may not be easy to recognize. And sometimes a SD sequence is not even in play, so that the numbers are quite useless. Let me know if you want to chat more about this. best, debbie

Link to this post | posted 08 Feb, 2025 15:39

debbie

Hi Kristen,
I will send you to the literature for this. When Dr. Lawrence adopted this method of SD determinations, he used the work of Dennis Kibler and Sam Karlin. I was under the impression that the spacer distance was between the end of the Shine DalGarno sequence and the start. Since SD sequence rarely match the lambda sequence, and the non-perfect matches have weighting schemes, i don't know how to count. the manual has a Kibler reference and here is a Karlin reference.

Go to the preference settings of DNA master and note that we have picked Kibler 6 and Karlin medium (quite arbitrarily). But the matrixes provided are quite involved.

Other questions:
The Z score uses the final score. But note that both numbers reflect similar relationships.

"Karlin Medium Shine-Dalgarno spacer matrix in the local settings of DNA Master" - the DNA Master setting (if you are using the most updated DNA Master are Karlin-Medium scores (unless you change your settings in the preferences.

Remember, both Kibler and Karlin are applying math to a 'best fit' situation. some may not be easy to recognize. And sometimes a SD sequence is not even in play, so that the numbers are quite useless.

Let me know if you want to chat more about this.
best,
debbie

Posted in: Choosing Start Sites → How is the RBS spacer distance counted?

Link to this post \| posted 06 Feb, 2025 18:04
debbie	Hi Holly, I recommend that you follow Sally's advice and call it an "ASCE ATPase". Thanks! debbie

Posted in: Cluster EA Annotation Tips → AAA ATPase or RecA recombinase?

Link to this post \| posted 05 Feb, 2025 19:45
debbie	Hi Sean, Yep. we have seen many examples of DNA Master not returning blast results for a few genes (even when every other gene in a genome blasts just fine). Just make a notation that blast results for those genes wouldn't save. We appreciate that you reBLASTed! You can move forward with your submission. best, debbie

Posted in: DNA Master → DNA Master will not save BLAST Results

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All posts created by debbie