SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 10 Apr, 2024 00:42
debbie	Hemiparasite afreise As of Dec 2022, are we leaving off the MuF part, based on this update from Debbie? https://seaphages.org/forums/topic/4628/ So now just: capsid maturation protease? (I am annotating Usavi (B1). The gene is here: https://phagesdb.org/genes/Usavi_CDS_10/) In the final annotation of Usavi, would it be Usavi_9 that is the example of this call, rather than Usavi_10? https://phagesdb.org/genes/Usavi_CDS_9/ YEP!!!

Link to this post | posted 10 Apr, 2024 00:42

Hemiparasite
afreise
As of Dec 2022, are we leaving off the MuF part, based on this update from Debbie? https://seaphages.org/forums/topic/4628/

So now just: capsid maturation protease?

(I am annotating Usavi (B1). The gene is here: https://phagesdb.org/genes/Usavi_CDS_10/)

In the final annotation of Usavi, would it be Usavi_9 that is the example of this call, rather than Usavi_10? https://phagesdb.org/genes/Usavi_CDS_9/

YEP!!!

Posted in: Cluster B Annotation Tips → Capsid maturation protease and MuF-like fusion protein

Link to this post \| posted 08 Apr, 2024 02:06
debbie	Hi Ombeline, I am not one to say that close enough is good enough, but in this case, I think the resemblance will do. I would call this slippage. The explanation is that for many years we believed that all siphoviridae had to have a programmed frameshift. In 2022 Alan Davidson's group published this paper to counter that. https://www.sciencedirect.com/science/article/pii/S0042682221002221 The sequence identified for the programmed frameshift is just too believable to not annotate it! best, debbie

Link to this post | posted 08 Apr, 2024 02:06

debbie

Hi Ombeline,
I am not one to say that close enough is good enough, but in this case, I think the resemblance will do. I would call this slippage.

The explanation is that for many years we believed that all siphoviridae had to have a programmed frameshift.
In 2022 Alan Davidson's group published this paper to counter that.
https://www.sciencedirect.com/science/article/pii/S0042682221002221

The sequence identified for the programmed frameshift is just too believable to not annotate it!

best,
debbie

Posted in: Cluster EA Annotation Tips → frame shift

Link to this post \| posted 05 Apr, 2024 18:14
debbie	Hi all, It does look like parts of GeneMark is down. I have written to their administrator to help to resolve. In the meantime, at least when I try, the Gene Mark server is working for GeneMark S. You can follow the direction from the guide found here: https://seaphagesbioinformatics.helpdocsonline.com/article-68 I think you can make all of the selections found in the guide except, the RBS model choice is no longer available. As for GeneMark host trained data, we will need to wait on the website for more information. i will continue to follow up. Best, debbie

Link to this post | posted 05 Apr, 2024 18:14

debbie

Hi all,
It does look like parts of GeneMark is down. I have written to their administrator to help to resolve.
In the meantime, at least when I try, the Gene Mark server is working for GeneMark S. You can follow the direction from the guide found here:
https://seaphagesbioinformatics.helpdocsonline.com/article-68
I think you can make all of the selections found in the guide except, the RBS model choice is no longer available.

As for GeneMark host trained data, we will need to wait on the website for more information. i will continue to follow up.

Best,
debbie

Posted in: PECAAN → GeneMarkS ?

Link to this post \| posted 22 Mar, 2024 16:55
debbie	debbie Hi Katie and Steve, The space where the DNA Master server lives is undergoing renovations. It is expected to be back next week. I'll keep you posted. debbie DNA Master's website is back up! 3/22/24 best, debbie

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 16 Mar, 2024 22:16
debbie	From Ann Findley: "I just checked with our computer science folks who were responsible for writing the code and administering the database. Unfortunately, when they went into the AWS account that was hosting the PET they were not able to recover the code. The latest information is that they are attempting to use an earlier version of PET to resurrect the tool. I am not certain of their timeline for completion." Best, debbie

Link to this post | posted 16 Mar, 2024 22:16

debbie

From Ann Findley:
"I just checked with our computer science folks who were responsible for writing the code and administering the database. Unfortunately, when they went into the AWS account that was hosting the PET they were not able to recover the code. The latest information is that they are attempting to use an earlier version of PET to resurrect the tool. I am not certain of their timeline for completion."
Best,
debbie

Posted in: General Message Board → Phage Enzyme Tools - PET2.0 - Down?

Link to this post \| posted 07 Mar, 2024 15:58
debbie	Hi Katie and Steve, The space where the DNA Master server lives is undergoing renovations. It is expected to be back next week. I'll keep you posted. debbie Edited 07 Mar, 2024 16:07

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 03 Mar, 2024 20:46
debbie	Fred, I wold not look to fill this space in the same way I might be inclined to do so at the right end of the genome. This space is likely part of the immunity cassette, and is likely expressed during lysogeny. I would not call this gene. debbie

Posted in: Cluster F Annotation Tips → 4 bp overlaps

Link to this post \| posted 03 Mar, 2024 11:03
debbie	Thank Claire, After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be! I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice. For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call. Please draw attention to these genes in your cover letter, so that the QCer can also evaluate. Anyone want to do some bench work?!! Best, debbie

Link to this post | posted 03 Mar, 2024 11:03

debbie

Thank Claire,
After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be!
I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice.

For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call.

Please draw attention to these genes in your cover letter, so that the QCer can also evaluate.

Anyone want to do some bench work?!!

Best,
debbie

Posted in: Cluster EE Annotation Tips → Genome Curation - a must read!

Link to this post \| posted 29 Feb, 2024 02:40
debbie	Check HHPred results. Yes, they are not in the typical synteny. Though it is not common, it is not uncommon. debbie

Posted in: Functional Annotation → Minor tail proteins far upstream of the tape measure protein?

Link to this post \| posted 22 Feb, 2024 21:48
debbie	I changed the approve function to say: "Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D)" debbie

Posted in: Functional Annotation → Metalloprotease without HEXXH motif?

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