SEA-PHAGES | All posts created by MSMC

Link to this post \| posted 17 Jun, 2020 13:31
MSMC	jawsWPI How hard and fast is the minor tail protein size range (1-3kb)? I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position. I see the same thing right now in an A3 phage. There are three minor tail proteins called as the first 3 genes: 426, 321 and 1200 bp respectively. The first two seem too short, none have any HHPRED data to support this function. It appears the functional assignment is based solely on synteny with other phages in the cluster, though only a few call these as minor tail proteins. I am thinking changing them to NKF.

Link to this post | posted 17 Jun, 2020 13:31

jawsWPI
How hard and fast is the minor tail protein size range (1-3kb)?
I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

I see the same thing right now in an A3 phage. There are three minor tail proteins called as the first 3 genes: 426, 321 and 1200 bp respectively. The first two seem too short, none have any HHPRED data to support this function. It appears the functional assignment is based solely on synteny with other phages in the cluster, though only a few call these as minor tail proteins. I am thinking changing them to NKF.

Posted in: Cluster A Annotation Tips → minor tail proteins

Link to this post \| posted 03 Jun, 2020 18:31
MSMC	I know that typically anything over about 30 bp overlap for genes should be looked at carefully. I've come across a cluster DU phage that has about a 100 bp overlap with the previous gene (see attached, HNH is gene 75). Is there an exception for significant overlaps with HNH endonucleases? 12Kb

Posted in: Choosing Start Sites → Significant overlap with HNH genes

Link to this post \| posted 27 Apr, 2020 00:48
MSMC	cdshaffer yes, two trivial things to try, 1) try a different browser sometimes this helps. 2) maximize the window size on the browser to fill the screen. 3) set zoom level to less than 100%, 4) Move to a computer with a large screen and try there (these problems usually show up on portables with small 12 or 13 inch screens). I never have had an issue in my office with my large 24 inch monitor Great, thanks for the suggestions, I'll give them a go. Thanks Chris!

Link to this post | posted 27 Apr, 2020 00:48

MSMC

cdshaffer
yes, two trivial things to try, 1) try a different browser sometimes this helps. 2) maximize the window size on the browser to fill the screen. 3) set zoom level to less than 100%, 4) Move to a computer with a large screen and try there (these problems usually show up on portables with small 12 or 13 inch screens). I never have had an issue in my office with my large 24 inch monitor

Great, thanks for the suggestions, I'll give them a go. Thanks Chris!

Posted in: PECAAN → problem with adding a gene

Link to this post \| posted 24 Apr, 2020 15:54
MSMC	cdshaffer For me when the top of the "add a gene window" is cut off it is because I have the zoom level set to magnify the page. This happens a lot as I typically have my pages default to 150% zoom or so. The tiny 3-line menu in the top right corner can be used to see and or change the current zoom level. Hi Chris, We tried changing the zoom level, but the "banner" on the top still obscures the box where you can put the gene start coordinate in. Do you know if there is another workaround for this issue? Thanks!

Link to this post | posted 24 Apr, 2020 15:54

MSMC

cdshaffer
For me when the top of the "add a gene window" is cut off it is because I have the zoom level set to magnify the page. This happens a lot as I typically have my pages default to 150% zoom or so. The tiny 3-line menu in the top right corner can be used to see and or change the current zoom level.

Hi Chris,

We tried changing the zoom level, but the "banner" on the top still obscures the box where you can put the gene start coordinate in. Do you know if there is another workaround for this issue? Thanks!

Posted in: PECAAN → problem with adding a gene

Link to this post \| posted 16 Apr, 2020 18:25
MSMC	welkin Hi Chris, All of the mass-spec evidence that we have indicates that when there are two start codons back-to-back, it is the downstream one that is correct. So sounds like you should go with the ATG in this case. Best, Welkin Does this apply to all codons (any combination of ATG/TTG/GTG back to back)? Thanks!

Posted in: Cluster CS Annotation Tips → TTG followed by ATG

Link to this post \| posted 08 Jan, 2020 18:20
MSMC	Annotating gene 33 in DumpsterDude. Two members in Pham, other member annotated as NKF. The HHPRED results indicate 100% probability match with PF14350.6 Beta_protein, 91% coverage, e-value 0. This beta_protein (http://pfam.xfam.org/family/PF14350.6) does appear to be found in T4 bacteriophages: "This family includes the beta protein from Bacteriophage T4, P13057. Beta protein prevents the gop protein, P13058 from killing the bacterial host cell [1]." I know this isn't on the approved list, and I don't think there's enough information here to warrant a function, but just wanted to put this here in case anyone ran across a similar type of gene.

Link to this post | posted 08 Jan, 2020 18:20

MSMC

Annotating gene 33 in DumpsterDude. Two members in Pham, other member annotated as NKF. The HHPRED results indicate 100% probability match with PF14350.6 Beta_protein, 91% coverage, e-value 0. This beta_protein (http://pfam.xfam.org/family/PF14350.6) does appear to be found in T4 bacteriophages:

"This family includes the beta protein from Bacteriophage T4, P13057. Beta protein prevents the gop protein, P13058 from killing the bacterial host cell [1]."

I know this isn't on the approved list, and I don't think there's enough information here to warrant a function, but just wanted to put this here in case anyone ran across a similar type of gene.

Posted in: Functional Annotation → Cluster DW - Beta protein?

Link to this post \| posted 17 Dec, 2019 18:58
MSMC	DanRussell Hi Evan, It seems like that Starterator report is now updated. My guess is that you did indeed catch it when the databases were slightly out-of-sync, since a new database version was posted last night. Usually when this happens it's just a matter of waiting for one of the tools to finishing processing, but we'll try to find a way to keep everything more in sync from here on. Can you access it now successfully? –Dan Yup, working now, thanks Dan!

Link to this post | posted 17 Dec, 2019 18:58

MSMC

DanRussell
Hi Evan,

It seems like that Starterator report is now updated. My guess is that you did indeed catch it when the databases were slightly out-of-sync, since a new database version was posted last night. Usually when this happens it's just a matter of waiting for one of the tools to finishing processing, but we'll try to find a way to keep everything more in sync from here on.

Can you access it now successfully?

–Dan

Yup, working now, thanks Dan!

Posted in: Starterator → Pham not showing up

Link to this post \| posted 17 Dec, 2019 16:35
MSMC	We’re doing a hackathon right now, and we’re having an issue with the starterator report for 97693. It gives us a page not found error, but there are 41 members in the pham, and the pham number is the same on PhagesDB (https://phagesdb.org/phams/97693/). Has this pham been updated in starterator but not in PhagesDB?

Posted in: Starterator → Pham not showing up

Link to this post \| posted 14 Nov, 2019 03:40
MSMC	Also, make sure you check with more than one enzyme. It's not uncommon for some enzymes to show few bands from digestion.

Posted in: Phage Discovery/Isolation → DNA Isolation from M. foliorum - any updates?

Link to this post \| posted 14 Nov, 2019 03:39
MSMC	DrCatalase Help, We got decent yields of DNA that and we tried to digest with NspI. the lanes are from two different phage lysates. Lanes: 1. DNA1 water 2. DNA1 water Buffer NspI (NEB 37 degrees 15 minutes) 3. DNA1 water Buffer 4. Ladder 5. DNA2 water 6. DNA2 water Buffer NspI (NEB 37 degrees 15 minutes) 7. DNA2 water Buffer We got no digestion except smearing in lane 6… we want to try again anyone have any suggestions? Thanks, Sean We've run into this issue before, it seems to be due to the conditions of the DNA sample after extraction - when we re-extracted using Phenol/Chloroform, we got digestion. It might be that you have either high concentration of salts or EDTA in the sample.

Link to this post | posted 14 Nov, 2019 03:39

MSMC

DrCatalase
Help,
We got decent yields of DNA that and we tried to digest with NspI. the lanes are from two different phage lysates.
Lanes:
1. DNA1 water
2. DNA1 water Buffer NspI (NEB 37 degrees 15 minutes)
3. DNA1 water Buffer
4. Ladder
5. DNA2 water
6. DNA2 water Buffer NspI (NEB 37 degrees 15 minutes)
7. DNA2 water Buffer

We got no digestion except smearing in lane 6… we want to try again anyone have any suggestions?
Thanks,
Sean

We've run into this issue before, it seems to be due to the conditions of the DNA sample after extraction - when we re-extracted using Phenol/Chloroform, we got digestion. It might be that you have either high concentration of salts or EDTA in the sample.

Posted in: Phage Discovery/Isolation → DNA Isolation from M. foliorum - any updates?

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