SEA-PHAGES | All posts created by debbie

← previous
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
next →

Link to this post \| posted 03 May, 2024 18:42
debbie	Be careful what you say about Fruitloop. Go to the paper and see the mas spec table and the map there. (when I looked, the paper doesn't match the GB file). There is a gene in there that you do want to call. i just don't have time right now to match it correctly. Let's touch base before you submit. best, debbie

Posted in: Gene or not a Gene → F1 cluster forward reverse or neither?

Link to this post \| posted 03 May, 2024 16:20
debbie	Hi Nikki, Mycobacteriophage Tweety has a paper that includes mass spec data. While the integrase and repressor have less sequence homology, that space in between may have enough similarity that you can draw some inferences that are applicable. Let me know what you think. https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13946 Best, debbie Edited 03 May, 2024 16:22

Posted in: Gene or not a Gene → F1 cluster forward reverse or neither?

Link to this post \| posted 24 Apr, 2024 19:04
debbie	You are welcome! debbie

Posted in: Cluster CS Annotation Tips → CS2 Holin Gene

Link to this post \| posted 24 Apr, 2024 17:02
debbie	Hi Dane, See the attached picture for why I would call a lot of theses proteins membrane proteins and not holins….. yet. Too many to choose from? debbie 392Kb

Posted in: Cluster CS Annotation Tips → CS2 Holin Gene

Link to this post \| posted 12 Apr, 2024 00:24
debbie	Hi Fernando, I think I want to stick with what is written in the Cluster O paper. There are 4 transmembrane proteins in the region downstream of lysin A and lysin B. I would call the 4 genes that hit Deep TMHMM transmembrane proteins - membrane proteins. Deep TMHMM is now the preferred method for transmembrane detection. (See Bioinformatics Guide.) And check out that data on phamerator!!! As to why holins may not be detected in HHPRed, I think that list could include that holins demonstrate a lot of diversity, holin activity may need more than one gene, holins are small proteins and must not be easy to crytallize and study. It is not uncommon to not find a hit to a holin. Best, debbie

Link to this post | posted 12 Apr, 2024 00:24

debbie

Hi Fernando,
I think I want to stick with what is written in the Cluster O paper. There are 4 transmembrane proteins in the region downstream of lysin A and lysin B.

I would call the 4 genes that hit Deep TMHMM transmembrane proteins - membrane proteins.
Deep TMHMM is now the preferred method for transmembrane detection. (See Bioinformatics Guide.)
And check out that data on phamerator!!!

As to why holins may not be detected in HHPRed, I think that list could include that holins demonstrate a lot of diversity, holin activity may need more than one gene, holins are small proteins and must not be easy to crytallize and study.

It is not uncommon to not find a hit to a holin.

Best,
debbie

Posted in: Cluster P Annotation Tips → Assignment of gp28 as holin

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

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!!!

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?

← previous
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
next →

Recent Activity

All posts created by debbie