SEA-PHAGES | All posts created by GregFrederick@letu.edu

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Link to this post \| posted 21 Feb, 2017 22:38
GregFrederick@letu.edu	GregFrederick@letu.edu Hi guys. I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?" QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed? Thanks for your help with this… I appreciate it. Greg Sorry for the repeat posts. We are just about done with the annotation phase and really want to be certain we have done everything required. Thank you.

Link to this post | posted 21 Feb, 2017 22:38

GregFrederick@letu.edu
Hi guys.

I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu

QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?"

QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed?

Thanks for your help with this… I appreciate it. Greg

Sorry for the repeat posts. We are just about done with the annotation phase and really want to be certain we have done everything required. Thank you.

Posted in: Notes and Final Files → Conserved Domain ID in notes

Link to this post \| posted 21 Feb, 2017 22:36
GregFrederick@letu.edu	Hi guys. I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?" QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed? Thanks for your help with this… I appreciate it. Greg

Link to this post | posted 21 Feb, 2017 22:36

GregFrederick@letu.edu

Hi guys.

I still need input on these questions (from above). If you would prefer to call me my number is 903.233.3354 or my email address is GregFrederick@letu.edu

QUESTION 1: "If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?"

QUESTION 2: "If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well?" HHPed?

Thanks for your help with this… I appreciate it. Greg

Posted in: Notes and Final Files → Conserved Domain ID in notes

Link to this post \| posted 16 Feb, 2017 16:08
GregFrederick@letu.edu	Welkin (or whomever): See question above. But I have one more… If we have a definite blastp match for feature function, do we need to list all the conserved domain id hits from Phamerator as well? Thanks again.

Posted in: Notes and Final Files → Conserved Domain ID in notes

Link to this post \| posted 16 Feb, 2017 15:48
GregFrederick@letu.edu	Welkin: One more question on this. The CDD is to be listed in the notes section within DNA Master under the FS: If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"? Thanks again for your input. We are just wanting to get everything done correctly "the first time" and obviously we have a bit of confusion on a few things… Thanks. Greg

Link to this post | posted 16 Feb, 2017 15:48

GregFrederick@letu.edu

Welkin: One more question on this.

The CDD is to be listed in the notes section within DNA Master under the FS:

If there is a CDD for a feature, do we also list that under F: as a "function" for the feature, even if it is not in the approved feature name table? Or do we list F: as "NA"?

Thanks again for your input. We are just wanting to get everything done correctly "the first time" and obviously we have a bit of confusion on a few things…

Thanks. Greg

Posted in: Notes and Final Files → Conserved Domain ID in notes

Link to this post \| posted 16 Feb, 2017 15:25
GregFrederick@letu.edu	Welkin Pope Nope, the tRNA cassettes are weird, and no you don't have to have a promoter for each of them or for each protein encoding gene interspersed within the cassette. We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close (take a look at the Ms). The only promoter rule is still about switching directions– presumably, switching transcriptional directions would still require two promoters even for tRNAs. Welkin: Based on this statement above ("We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close" ) ….It seems we should delete the tRNA gene. Could you take a look at the image linked in my post above and let me know your thoughts on how to deal with this specific situation? Thank you. G Edited 16 Feb, 2017 15:27

Link to this post | posted 16 Feb, 2017 15:25

GregFrederick@letu.edu

Welkin Pope
Nope, the tRNA cassettes are weird, and no you don't have to have a promoter for each of them or for each protein encoding gene interspersed within the cassette. We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close (take a look at the Ms). The only promoter rule is still about switching directions– presumably, switching transcriptional directions would still require two promoters even for tRNAs.

Welkin: Based on this statement above ("We tend to steer clear of a tRNA and a protein occupying the same space, but there are definitely genomes where they get pretty close" )

….It seems we should delete the tRNA gene.

Could you take a look at the image linked in my post above and let me know your thoughts on how to deal with this specific situation? Thank you. G

Edited 16 Feb, 2017 15:27

Posted in: tRNAs → How close can one pack protein and tRNA's genes

Link to this post \| posted 16 Feb, 2017 15:17
GregFrederick@letu.edu	GregFrederick@letu.edu To follow up with this discussion, we have a tRNA gene identified by Aragorn on the +3 frame and a clear ORF on the -2 frame. In other words, they are in opposite orientation on the genome. However, the both look very "REAL". The Frames output is below. https://drive.google.com/open?id=0B_7KYneUM8kdVWRKWjJrQlFBajQ We are planning to call both unless we hear otherwise here. Let me know your thoughts. Thank you. GF To clarify: The ORF and the tRNA gene in question are overlapping, and on the opposite strands. See the picture of the region in the image at the link. I did not see a reply to this question. We are about finished with the annotation portion of the course. However, we are uncertain how to deal with this region. Thoughts? Edited 16 Feb, 2017 15:22

Link to this post | posted 16 Feb, 2017 15:17

GregFrederick@letu.edu

GregFrederick@letu.edu
To follow up with this discussion, we have a tRNA gene identified by Aragorn on the +3 frame and a clear ORF on the -2 frame. In other words, they are in opposite orientation on the genome.

However, the both look very "REAL". The Frames output is below.

https://drive.google.com/open?id=0B_7KYneUM8kdVWRKWjJrQlFBajQ

We are planning to call both unless we hear otherwise here.

Let me know your thoughts. Thank you. GF

To clarify: The ORF and the tRNA gene in question are overlapping, and on the opposite strands. See the picture of the region in the image at the link.

I did not see a reply to this question. We are about finished with the annotation portion of the course. However, we are uncertain how to deal with this region.

Thoughts?

Edited 16 Feb, 2017 15:22

Posted in: tRNAs → How close can one pack protein and tRNA's genes

Link to this post \| posted 08 Feb, 2017 22:55
GregFrederick@letu.edu	cdshaffer Ok well it appears that flaverint does not crash my current "development" version of Starterator. So I can generate a whole phage report using it. The problem with the development version is that I have taken out much of the code that generates the summary text below the graph in anticipation of adding improved versions along the lines of the improvements to the single pham reports. Consequently the whole phage report that comes out has all the graphics but none of the summary text. So, no counting which starts are annotated and/or conserved and no list of base locations for the various starts in the phage being analyzed, this means the online version is still better for all that info. The good news is that these whole phage reports do have the part of the PDF that you need to upload to PECAAN and PECAAN will have the links to the online versions. Below are links to download the whole phage report for the crashing phage mentioned above as generated by the development version of starterator (for anyone interested the current development version is this branch of my person github repo). Whole phage pdf report for Aggie using development version of Starterator Whole phage pdf report for Flaverint using development version of Starterator Whole phage pdf report for Mattes using development version of Starterator Whole phage pdf report for Andies using development version of Starterator Whole phage pdf report for Philonius using development version of Starterator Whole phage pdf report for Aroostook using development version of Starterator CHRIS!!!!! YOU ARE AWESOME!!!! Thank you so much!!!! gf

Link to this post | posted 08 Feb, 2017 22:55

GregFrederick@letu.edu

cdshaffer
Ok well it appears that flaverint does not crash my current "development" version of Starterator. So I can generate a whole phage report using it. The problem with the development version is that I have taken out much of the code that generates the summary text below the graph in anticipation of adding improved versions along the lines of the improvements to the single pham reports.

Consequently the whole phage report that comes out has all the graphics but none of the summary text. So, no counting which starts are annotated and/or conserved and no list of base locations for the various starts in the phage being analyzed, this means the online version is still better for all that info. The good news is that these whole phage reports do have the part of the PDF that you need to upload to PECAAN and PECAAN will have the links to the online versions.

Below are links to download the whole phage report for the crashing phage mentioned above as generated by the development version of starterator (for anyone interested the current development version is this branch of my person github repo).
Whole phage pdf report for Aggie using development version of Starterator

Whole phage pdf report for Flaverint using development version of Starterator

Whole phage pdf report for Mattes using development version of Starterator

Whole phage pdf report for Andies using development version of Starterator

Whole phage pdf report for Philonius using development version of Starterator

Whole phage pdf report for Aroostook using development version of Starterator

CHRIS!!!!! YOU ARE AWESOME!!!! Thank you so much!!!! gf smile

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 02 Feb, 2017 19:41
GregFrederick@letu.edu	To follow up with this discussion, we have a tRNA gene identified by Aragorn on the +3 frame and a clear ORF on the -2 frame. In other words, they are in opposite orientation on the genome. However, the both look very "REAL". The Frames output is below. https://drive.google.com/open?id=0B_7KYneUM8kdVWRKWjJrQlFBajQ We are planning to call both unless we hear otherwise here. Let me know your thoughts. Thank you. GF Edited 16 Feb, 2017 15:20

Link to this post | posted 02 Feb, 2017 19:41

GregFrederick@letu.edu

To follow up with this discussion, we have a tRNA gene identified by Aragorn on the +3 frame and a clear ORF on the -2 frame. In other words, they are in opposite orientation on the genome.

However, the both look very "REAL". The Frames output is below.

https://drive.google.com/open?id=0B_7KYneUM8kdVWRKWjJrQlFBajQ

We are planning to call both unless we hear otherwise here.

Let me know your thoughts. Thank you. GF

Edited 16 Feb, 2017 15:20

Posted in: tRNAs → How close can one pack protein and tRNA's genes

Link to this post \| posted 31 Jan, 2017 23:20
GregFrederick@letu.edu	The password is "phage". There is a document here with details: http://seaphages.org/media/docs/Server_and_databases_for_Phamerator_and_Starterator.docx

Posted in: Phamerator → Install Guest Additions to VM ---- Without "SEAFaculty Login ability"

Link to this post \| posted 27 Jan, 2017 17:49
GregFrederick@letu.edu	FOLLOW UP FROM OUR I.T. TEAM: The particular service that was causing the issue for us on Windows 10 clients was "Device Guard." A quick way to find out if it is enabled is to run msinfo32 on the Windows 10 computer having problems: https://www.tenforums.com/tutorials/68926-device-guard-verify-if-enabled-disabled-windows-10-a.html A PowerShell script is available from Microsoft to disable this feature: https://www.microsoft.com/en-us/download/details.aspx?id=53337 I would recommend that anyone having problems consult their IT department. It may take someone who is familiar with the workings of PowerShell to initiate this script with the correct "switches."

Link to this post | posted 27 Jan, 2017 17:49

GregFrederick@letu.edu

FOLLOW UP FROM OUR I.T. TEAM:

The particular service that was causing the issue for us on Windows 10 clients was "Device Guard."

A quick way to find out if it is enabled is to run msinfo32 on the Windows 10 computer having problems: https://www.tenforums.com/tutorials/68926-device-guard-verify-if-enabled-disabled-windows-10-a.html

A PowerShell script is available from Microsoft to disable this feature: https://www.microsoft.com/en-us/download/details.aspx?id=53337

I would recommend that anyone having problems consult their IT department. It may take someone who is familiar with the workings of PowerShell to initiate this script with the correct "switches."

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

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