SEA-PHAGES | All posts created by vbrownk

Link to this post \| posted 11 Mar, 2022 20:22
vbrownk	Makes sense for Gene 21 For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. - VBK Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 11 Mar, 2022 20:22

Makes sense for Gene 21
For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. smile

- VBK

Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein,

Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it.

This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also.
https://seaphages.org/forums/topic/5009/

Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck!

debbie

Posted in: Cluster DR Annotation Tips → Tail Assembly Chaperone

Link to this post \| posted 11 Mar, 2022 20:22
vbrownk	Makes sense for Gene 21 For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. - VBK Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 11 Mar, 2022 20:22

vbrownk

Posted in: Cluster DR Annotation Tips → Tail Assembly Chaperone

Link to this post \| posted 07 Mar, 2022 16:40
vbrownk	See attached image. I am having trouble convincing myself that Fresco_21 / Fresco_22 have the slippage/frameshift in the tail assembly chaperones, because a TGA stop happens too early in the 1st ORF(Fresco_21) making that frameshift at the - gggg - into the 2nd ORF(Fresco_22) unproductive. Both NHagos and Sour align well to Fresco_21 (frame 1) and Fresco_22 (frame 3 only), but that would require a 2-frame shift, and the only viable place I see for slippage (– gggg &ndash is downstream of the TGA. See attached image worth 1,000 poorly written words. Thoughts? -VBK 186Kb

Link to this post | posted 07 Mar, 2022 16:40

vbrownk

See attached image.
I am having trouble convincing myself that Fresco_21 / Fresco_22 have the slippage/frameshift in the tail assembly chaperones, because a TGA stop happens too early in the 1st ORF(Fresco_21) making that frameshift at the - gggg - into the 2nd ORF(Fresco_22) unproductive. Both NHagos and Sour align well to Fresco_21 (frame 1) and Fresco_22 (frame 3 only), but that would require a 2-frame shift, and the only viable place I see for slippage (– gggg &ndash smile

is downstream of the TGA. See attached image worth 1,000 poorly written words. smile

Thoughts?
-VBK

Posted in: Cluster DR Annotation Tips → Tail Assembly Chaperone

Link to this post \| posted 05 Aug, 2021 22:20
vbrownk	vbrownk I am getting this same error now, just like Tamarah's. Error (16) retrieving results for RID … OK WELL … this resolved when I switched from university wifi to ethernet. Whew! -VBK

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 05 Aug, 2021 21:20
vbrownk	I am getting this same error now, just like Tamarah's. Error (12) retrieving results for RID … I have a tiny genome with only 26 ORFs, but am using the Export (New SEA format) file export … I never go this with the regular export of CDS Full Annotations - should I use that export type instead? I followed the instructions exactly from here to transfer from PECAAN to DNAmaster: https://pitt.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=88be7083-c942-4e21-97f4-ac010116edae. This the 1st time I've used the "new" export file and the 1st time this has happened. Any advice? Use the other, not "new" format? Thanks! -VBK

Link to this post | posted 05 Aug, 2021 21:20

vbrownk

I am getting this same error now, just like Tamarah's.
Error (12) retrieving results for RID …

I have a tiny genome with only 26 ORFs, but am using the Export (New SEA format) file export … I never go this with the regular export of CDS Full Annotations - should I use that export type instead? I followed the instructions exactly from here to transfer from PECAAN to DNAmaster:

https://pitt.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=88be7083-c942-4e21-97f4-ac010116edae.

This the 1st time I've used the "new" export file and the 1st time this has happened.
Any advice? Use the other, not "new" format?
Thanks!
-VBK

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 19 Apr, 2018 17:16
vbrownk	Welkin Pope Yes. Your IT people can install DNA Master and give it admin rights for all users regardless of their privileges. It will run fine. Best, Welkin I have DNAMaster installed on Windows 10, selected "Run this program as an administrator", changes settings for all users. But my standard users are still not able to log in. Please assist. Thanks. Christal

Posted in: DNA Master → Running with Administrator Privileges

Link to this post \| posted 28 Mar, 2017 11:52
vbrownk	My Phamerator ran a database update, and now it's hung up: Database Setup Required. Please enter your root database password. ? What's this? Also asked on main seahages page (before finding this forum!). Thanks, VBK

Posted in: SEA-PHAGES Virtual Machine → No Ubuntu 64-bit option when installing 2017 VM on Windows

Link to this post \| posted 28 Mar, 2017 11:39
vbrownk	My Phamerator claims to have been updating the database, but now it is asking from my root database password -? What is that? Thanks, Victoria

Posted in: Phamerator → Force A Database Update? How?

Link to this post \| posted 02 Mar, 2017 19:15
vbrownk	Question! (Also posted this on the external questions because I forgot my login). In viral genes, when there is start configuration like this: ATGATG … Is there some rule in bacteria/viruses that the second ATG is correct? We have several ORFs where the annotated START in other genomes (thus in STARTerator) choose ATG #2; however, ATG #1 would allow for a 4bp overlap with the upstream ORF, and if the subject in question already has its STOP overlapped 4bp with the downstream ORF - this would be a beautiful operon, but in direct conflict with STARTerator. -Victoria Kalah2_draft start@ 51741 vs. 51738 (REV). Pham 8105

Link to this post | posted 02 Mar, 2017 19:15

vbrownk

Question!
(Also posted this on the external questions because I forgot my login).

In viral genes, when there is start configuration like this:
ATGATG …
Is there some rule in bacteria/viruses that the second ATG is correct?

We have several ORFs where the annotated START in other genomes (thus in STARTerator) choose ATG #2; however, ATG #1 would allow for a 4bp overlap with the upstream ORF, and if the subject in question already has its STOP overlapped 4bp with the downstream ORF - this would be a beautiful operon, but in direct conflict with STARTerator.

-Victoria
Kalah2_draft
start@ 51741 vs. 51738 (REV).
Pham 8105

Posted in: Choosing Start Sites → Two consecutive ATG start sites

Link to this post \| posted 09 Feb, 2017 09:57
vbrownk	Thank you! cdshaffer The pdf library in phamerator is not very good so if you save a map from phamerator directly to PDF and try to print in large form it does not work well. Here is the recommended protocol I give my students: 1. Open phamerator and create your map. 2. Edit the view menu to set what is shown and not shown to suit your purpose 3. Save as a SVG from phamerator. 4. Transfer the file as needed to a computer which has Inkscape installed. (Inkscpe is a free to download graphics program that works kind of like Illustrator. There are versions for all platforms) 5. Open the file in Inkscape and use save as… to save in PDF format 6. Open the PDF version of the file in whatever program you are using to create your poster 7. Typically students are using Powerpoint to create a giant slide, in which case I tell them to use the Insert menu -> photo -> picture from file to select the PDF. Then resize the map to fit the size of the poster.

Link to this post | posted 09 Feb, 2017 09:57

vbrownk

Thank you!

cdshaffer
The pdf library in phamerator is not very good so if you save a map from phamerator directly to PDF and try to print in large form it does not work well.

Here is the recommended protocol I give my students:

1. Open phamerator and create your map.
2. Edit the view menu to set what is shown and not shown to suit your purpose
3. Save as a SVG from phamerator.
4. Transfer the file as needed to a computer which has Inkscape installed. (Inkscpe is a free to download graphics program that works kind of like Illustrator. There are versions for all platforms)
5. Open the file in Inkscape and use save as… to save in PDF format
6. Open the PDF version of the file in whatever program you are using to create your poster
7. Typically students are using Powerpoint to create a giant slide, in which case I tell them to use the Insert menu -> photo -> picture from file to select the PDF. Then resize the map to fit the size of the poster.

Posted in: Phamerator → Printing phamerator maps

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