SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 15 Jun, 2023 02:50
debbie	The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in? This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips. Hi all, This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments! debbie

Link to this post | posted 15 Jun, 2023 02:50

The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in?
This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips.

Hi all,
This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments!
debbie

Posted in: Cluster F Annotation Tips → Immunity Repressor and CRO starts

Link to this post \| posted 15 Jun, 2023 02:10
debbie	Kirk, This pham is quite messy. I would call the longest ORF and call the r-h-h for this one even though other members of this pham cannot call it. debbie

Posted in: Functional Annotation → Usavi_draft_70: potentially ribbon-helix-helix?

Link to this post \| posted 15 Jun, 2023 00:33
debbie	I would call this a phosphoesterase too. debbie

Posted in: Functional Annotation → Phosphoesterase or metallophosphoesterase? A clarification question

Link to this post \| posted 14 Jun, 2023 18:16
debbie	Please Read! https://pubmed.ncbi.nlm.nih.gov/24335314/

Posted in: Cluster M Annotation Tips → Suggested Reading: tRNAs in Cluster M phages

Link to this post \| posted 07 Jun, 2023 23:30
debbie	Rick, I think that this version of TAC matches L5's -1 frameshift. https://seaphagesbioinformatics.helpdocsonline.com/article-54 G_GG.G_GA. Wanna check? debbie

Posted in: Cluster EA Annotation Tips → frame shift

Link to this post \| posted 07 Jun, 2023 20:23
debbie	Lee, The confusing part of Kathleen's post is the sentence that states "But we don't understand why Starterator didn't call the most annotated start." But she is here today so we are able to discuss. The reason that Starterator doesn't make the right call is becuase it only reports what is in in the files submitted to phamerator. –Meaning in this particular case, Frankenweenie's auto-annotated is not what others ID'd as the best start to call. In fact, Kathleen and her students went to Starterator to justify making a change. That sentence in Starterator is to be coupled with the yellow line in the Frankenweenie graph and recogonized as in DRAFT form. What Kathleen and her students wanted was for Starterator to make the right call. Technically, it makes NO calls and just reports what was called (making human calls green and auto calls yellow).

Link to this post | posted 07 Jun, 2023 20:23

debbie

Lee,
The confusing part of Kathleen's post is the sentence that states "But we don't understand why Starterator didn't call the most annotated start." But she is here today so we are able to discuss.
The reason that Starterator doesn't make the right call is becuase it only reports what is in in the files submitted to phamerator. –Meaning in this particular case, Frankenweenie's auto-annotated is not what others ID'd as the best start to call. In fact, Kathleen and her students went to Starterator to justify making a change. That sentence in Starterator is to be coupled with the yellow line in the Frankenweenie graph and recogonized as in DRAFT form. What Kathleen and her students wanted was for Starterator to make the right call. Technically, it makes NO calls and just reports what was called (making human calls green and auto calls yellow).

Posted in: Cluster BM Annotation Tips → Interpreting Starterator data in BM cluster phages

Link to this post \| posted 06 Jun, 2023 02:55
debbie	Hi all, There are (were) 2 strains of Arthrobacter globiformis from NRRL at Pitt that got distributed as A. globiformis NRRL B- 2979 SEA. They are A. globiformis NRRL B- 2979 SEA and A. globiformis NRRL B-2880 SEA. It is believed that one of the errors occurred in Spring shipments of 2019. However, we can't be sure, so we are asking that all A. globi strains be tested. Both strains have been sequenced and primers are designed to detect each strain. Protocol is attached here. First step is that if you have A. globiformis at your institution, please verify which one you have using the attached protocol. Second step, check phagesDB that all phages found on that strain are entered correctly. If not please make changes. If the number of phage hosts to be changed is small, use "Modify Phage" to correct. If you have many phage hosts to correct, you can send Dan (dar78@pitt.edu) a message to get the entries changed in bulk. Please send an email to inof@seaphages.org with your questions. Thanks! debbie Edited 13 Jun, 2023 12:52 1.01Mb

Link to this post | posted 06 Jun, 2023 02:55

debbie

Hi all,
There are (were) 2 strains of Arthrobacter globiformis from NRRL at Pitt that got distributed as A. globiformis NRRL B- 2979 SEA. They are A. globiformis NRRL B- 2979 SEA and A. globiformis NRRL B-2880 SEA. It is believed that one of the errors occurred in Spring shipments of 2019. However, we can't be sure, so we are asking that all A. globi strains be tested.
Both strains have been sequenced and primers are designed to detect each strain. Protocol is attached here.
First step is that if you have A. globiformis at your institution, please verify which one you have using the attached protocol.
Second step, check phagesDB that all phages found on that strain are entered correctly. If not please make changes. If the number of phage hosts to be changed is small, use "Modify Phage" to correct. If you have many phage hosts to correct, you can send Dan (dar78@pitt.edu) a message to get the entries changed in bulk.
Please send an email to inof@seaphages.org with your questions.
Thanks!
debbie

Edited 13 Jun, 2023 12:52

Posted in: Phage Discovery/Isolation → Confirmation of A. globiformis strain sent from Pitt

Link to this post \| posted 06 Jun, 2023 01:20
debbie	I agree it is not enough yet. but good to make the post. debbie

Posted in: Request a new function on the SEA-PHAGES official list → ribosomal protein l7/l12

Link to this post \| posted 04 Jun, 2023 17:18
debbie	Dan, What kind of images? Do you mean the plaque or EM pic on phagesDB or something else? debbie

Posted in: Data Upload Questions → Image file size

Link to this post \| posted 02 Jun, 2023 00:26
debbie	Fred, the program needs to update to get to the right version for setting preferences. if the progam isn't avilable at cobamide…. Go the DNA master page on phagesDB. Click on the word "here" in the second sentence to download the install program. debbie

Posted in: DNA Master → DNA Master Preferences Issue

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All posts created by debbie