SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 19 Nov, 2021 17:22
debbie	Thanks Chris!

Posted in: tRNAs → Tomas tRNA error

Link to this post \| posted 19 Nov, 2021 16:11
debbie	Lee, Great forum post. Thanks for having a complete set of data. You are correct that the checker message is confusing. Thanks for reviewing. I think that this tRNA is legit and the coordinates are 99206-99276, tRNA-Gln(gat). There is no way around this in the checker and I am will contact Christian to push this one through. Sometimes, you may receive additional error message, but just ignore. it is ready to go in. Best, debbie

Link to this post | posted 19 Nov, 2021 16:11

debbie

Lee,
Great forum post.
Thanks for having a complete set of data.
You are correct that the checker message is confusing. Thanks for reviewing. I think that this tRNA is legit and the coordinates are 99206-99276, tRNA-Gln(gat). There is no way around this in the checker and I am will contact Christian to push this one through. Sometimes, you may receive additional error message, but just ignore. it is ready to go in.
Best,
debbie

Posted in: tRNAs → Tomas tRNA error

Link to this post \| posted 12 Nov, 2021 14:34
debbie	Hi Amanda, Kyle's answer reflects our experiences too. So while I am not sure the details for how best to get phage yields from any of these hosts, figuring that out is legit. The caveat, I think, would be if any are 'ready' for use in the student lab. For us the experience is that we don't have enough experience with any of them to know what best practice is. Denise Monti has used Corynebacterium in the classroom, so you might want to ask her. Good Luck! debbie

Link to this post | posted 12 Nov, 2021 14:34

debbie

Hi Amanda,
Kyle's answer reflects our experiences too. So while I am not sure the details for how best to get phage yields from any of these hosts, figuring that out is legit. The caveat, I think, would be if any are 'ready' for use in the student lab. For us the experience is that we don't have enough experience with any of them to know what best practice is. Denise Monti has used Corynebacterium in the classroom, so you might want to ask her.
Good Luck!
debbie

Posted in: Phage Discovery/Isolation → New hosts - human microbiome

Link to this post \| posted 10 Nov, 2021 20:53
debbie	HI! Search the Approved Funnction list for "HIT domain" and you will find "histidine triad nucleotide binding protein" as a good choice for what to call this protein. Make sense? Thanks for the inquiry, debbie

Posted in: Cluster F Annotation Tips → HIT Family Protein

Link to this post \| posted 03 Nov, 2021 22:49
debbie	Hi Jess, Cool genome. I can't answer your question out of context of the entire genome. Tell me if yo agree with my interpretations. Here is what I see so far, you have a small genome phage that is likely a podoviridae. You have only provided one virion particle. do you have more. If not can you get more particles photographed. Also, I note that you have a thumbnail uploaded - which is great!!!, but not a 'raw' data file uploaded. That file can be very helpful, so please upload it. Because it is a podo, we haven't thought very much about the structures at the portal. Could the upper collar be the portal? Your phage is like phi29, S. aureus phage P68 and maybe Streptococcus phage C1. Here is a lovely paper about the structure of the Staph aureus phage. https://www.science.org/doi/10.1126/sciadv.aaw7414 I don't think there is anything difficult about this phage, but we don't have a good handle on what to call the structural pieces that are identified. If you could find the papers about phi29 and maybe even C1, we could put the pieces together and identify the best names for the proteins. Maybe we could set up a time to talk. Cool beans! debbie

Link to this post | posted 03 Nov, 2021 22:49

debbie

Hi Jess,
Cool genome. I can't answer your question out of context of the entire genome. Tell me if yo agree with my interpretations.
Here is what I see so far, you have a small genome phage that is likely a podoviridae. You have only provided one virion particle. do you have more. If not can you get more particles photographed. Also, I note that you have a thumbnail uploaded - which is great!!!, but not a 'raw' data file uploaded. That file can be very helpful, so please upload it.

Because it is a podo, we haven't thought very much about the structures at the portal. Could the upper collar be the portal?

Your phage is like phi29, S. aureus phage P68 and maybe Streptococcus phage C1. Here is a lovely paper about the structure of the Staph aureus phage.
https://www.science.org/doi/10.1126/sciadv.aaw7414

I don't think there is anything difficult about this phage, but we don't have a good handle on what to call the structural pieces that are identified. If you could find the papers about phi29 and maybe even C1, we could put the pieces together and identify the best names for the proteins.

Maybe we could set up a time to talk.
Cool beans!
debbie

Posted in: Functional Annotation → Upper and lower collar proteins

Link to this post \| posted 01 Nov, 2021 20:56
debbie	Hi Chris, I want this to slip, and i think that it has to slip, BUT it does not fit any published programmed ribosomal slippages to date. I would leave it as 2 separate orfs. But if someone want to talk me into calling it, I am all ears! debbie

Posted in: Frameshifts and Introns → TAC frameshift in singleton

Link to this post \| posted 01 Nov, 2021 01:06
debbie	Sorry for the delay in this response. I think that the hits to levanase and hydrolase suggest that this could be a minor tail protein. It is not in a canonical location so this gets a bit tricky to call. Howver, becsuse it is very similar to BENtherdunthat_gp35 that is in a more canonical space makes me think that it could indeed be a minor tail.

Posted in: Functional Annotation → Minor tail protein in the far left arm of CS3 phages?

Link to this post \| posted 14 Oct, 2021 20:12
debbie	Amanda, HI! Sorry for the delay in my response too! Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output. Use the cover sheet to describe what you have done and all should work out. debbie

Posted in: Notes and Final Files → Question about notes template

Link to this post \| posted 17 Sep, 2021 16:24
debbie	Hi all, My last posts were misguided. It was the license problem. GeneMark is back on line! debbie

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 16 Sep, 2021 21:12
debbie	I just talked to Christian and he suggested the simplest explanation is the Preference Settings in the Secure Connections panel are not set properly. See the attached picture for what they should look like. Going forward, would you let me know if you still have problems what DNA master build number you are using. (The latest build that i have is 2704.) Thanks! 164Kb

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

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