SEA-PHAGES | All posts created by fogartym1

Link to this post \| posted 29 Mar, 2016 11:45
fogartym1	Thank you both - this is very helpful.

Posted in: Gene or not a Gene → Cluster B gene with no coding potential

Link to this post \| posted 15 Mar, 2016 17:19
fogartym1	Phamerator map of the area 57Kb

Posted in: Gene or not a Gene → Cluster B gene with no coding potential

Link to this post \| posted 15 Mar, 2016 17:19
fogartym1	When reviewing a student’s annotation, we came across the following situation where a student had added a gene: Below is the evidence used to call the gene and I would appreciate an expert opinion on the call. 1. There was a large gap ( > 400 bp) between genes 9 + 10 in Iridoclysis 2. In at least three other cluster B phages a similar gap has been filled by a gene (see phamerator map below). The gene was added and the following information was noted: Blast: 1:1 alignment with gp10 of 3 other phages. RBS Final SD – 6.354; Z = 1.399 (not wonderful). FS: According to phamerator, a similar gene in other phage is assigned a function of HNH endonuclease, also there is a ~ 60 bp hit on hhpred for a HnH endonuclease (99% probablility) and a hit for a HNH endonuclease domain when blasted using phages db. An additional piece of evidence, we uploaded the Fasta sequence to Starterator (since it is an unphamerated gene) and got agreement with our start site call. This all seems like good evidence except for one thing: Coding Potential in Genemark (S, smeg and TB) is pitiful! (see attached coding potential file). My question - so does that mean, this gene cannot / should not be added? If I had been doing the annotation, I might not have ever added this gene based on the GeneMark files. Edited 15 Mar, 2016 17:38 84Kb

Link to this post | posted 15 Mar, 2016 17:19

fogartym1

When reviewing a student’s annotation, we came across the following situation where a student had added a gene:
Below is the evidence used to call the gene and I would appreciate an expert opinion on the call.
1. There was a large gap ( > 400 bp) between genes 9 + 10 in Iridoclysis
2. In at least three other cluster B phages a similar gap has been filled by a gene (see phamerator map below).
The gene was added and the following information was noted:
Blast: 1:1 alignment with gp10 of 3 other phages.
RBS Final SD – 6.354; Z = 1.399 (not wonderful).
FS: According to phamerator, a similar gene in other phage is assigned a function of HNH endonuclease, also there is a ~ 60 bp hit on hhpred for a HnH endonuclease (99% probablility) and a hit for a HNH endonuclease domain when blasted using phages db.
An additional piece of evidence, we uploaded the Fasta sequence to Starterator (since it is an unphamerated gene) and got agreement with our start site call.
This all seems like good evidence except for one thing:
Coding Potential in Genemark (S, smeg and TB) is pitiful! (see attached coding potential file).

My question - so does that mean, this gene cannot / should not be added?
If I had been doing the annotation, I might not have ever added this gene based on the GeneMark files.

Edited 15 Mar, 2016 17:38

Posted in: Gene or not a Gene → Cluster B gene with no coding potential

Link to this post \| posted 01 Feb, 2016 22:13
fogartym1	Tamarah Adair We are running DNA Master within the WINE configuration. The installer has been copied and you should be able to get to it from this link. https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz Our contact is in Student Technology Services. He installs the DNA Master on the Macs in the lab at the beginning of the spring semester. If there are updates he incorporates these. I'm sure he would be glad to answer any questions you might have. Thanks so much for this - so happy to be able to run this on my mac.

Link to this post | posted 01 Feb, 2016 22:13

fogartym1

Tamarah Adair
We are running DNA Master within the WINE configuration.
The installer has been copied and you should be able to get to it from this link.
https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz

Our contact is in Student Technology Services. He installs the DNA Master on the Macs in the lab at the beginning of the spring semester. If there are updates he incorporates these. I'm sure he would be glad to answer any questions you might have.

Thanks so much for this - so happy to be able to run this on my mac.

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 01 Feb, 2016 22:03
fogartym1	GregFrederick@letu.edu fogartym1 We have been listening back to the live stream from our training week - it is an excellent resource for jogging the memory: On the 12 / 8 stream at ~ 4hr:45 minutes Welkin introduces Starterator. I think that Steve talks about Phamerator on the same day but we have not gotten that far yet!! Also - http://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf The guide is useful. Thanks. I think this was the day I was sick in the morning and I apparently missed a lot. Can you help me find the link to the "live stream". I'm not finding it as I scan SEAPhages.org pages. Thanks in advance. Greg Hi Greg: It is on this page from the workshop http://seaphages.org/meetings/10/ It reads view the live stream here … This is the direct link http://mediasiteex.hhmi.org/Mediasite/Catalog/Full/672215ce45df45caa93499b86d49c64821

Link to this post | posted 01 Feb, 2016 22:03

fogartym1

GregFrederick@letu.edu
fogartym1
We have been listening back to the live stream from our training week - it is an excellent resource for jogging the memory:
On the 12 / 8 stream at ~ 4hr:45 minutes Welkin introduces Starterator. I think that Steve talks about Phamerator on the same day but we have not gotten that far yet!!

Also - http://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf

The guide is useful. Thanks.

I think this was the day I was sick in the morning and I apparently missed a lot. Can you help me find the link to the "live stream". I'm not finding it as I scan SEAPhages.org pages.

Thanks in advance. Greg

Hi Greg:
It is on this page from the workshop
http://seaphages.org/meetings/10/

It reads view the live stream here …

This is the direct link
http://mediasiteex.hhmi.org/Mediasite/Catalog/Full/672215ce45df45caa93499b86d49c64821

Posted in: Phamerator → Tutorial on Phamerator and Starterator Use?

Link to this post \| posted 30 Jan, 2016 16:17
fogartym1	GregFrederick@letu.edu Are there tutorials available for these two softwares? Those for DM are excellent for helping students (and new faculty) walk through issues that come up. If there are video or text tutorials available for the software inside the VM that would be really wonderful? Show me the way! (I'm almost certain they are out there. So please help me find them!) Thanks. We have been listening back to the live stream from our training week - it is an excellent resource for jogging the memory: On the 12 / 8 stream at ~ 4hr:45 minutes Welkin introduces Starterator. I think that Steve talks about Phamerator on the same day but we have not gotten that far yet!! Also - http://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf Edited 30 Jan, 2016 21:53

Link to this post | posted 30 Jan, 2016 16:17

fogartym1

GregFrederick@letu.edu
Are there tutorials available for these two softwares? Those for DM are excellent for helping students (and new faculty) walk through issues that come up.

If there are video or text tutorials available for the software inside the VM that would be really wonderful? Show me the way! (I'm almost certain they are out there. So please help me find them!)

Thanks.

We have been listening back to the live stream from our training week - it is an excellent resource for jogging the memory:
On the 12 / 8 stream at ~ 4hr:45 minutes Welkin introduces Starterator. I think that Steve talks about Phamerator on the same day but we have not gotten that far yet!!

Also - http://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf

Edited 30 Jan, 2016 21:53

Posted in: Phamerator → Tutorial on Phamerator and Starterator Use?

Link to this post \| posted 30 Jan, 2016 16:11
fogartym1	Lee Hughes joyous726 We have something strange going on when we compare our auto-annotated Blast file in DNA master to what's in phamerator and starterator for ShiaLaBeouf_Draft. The gene product numbers/features don't align like they do for other phage genomes. It is probably because the auto-annotations came up with different results (yours compared to the one done for the phamerator file). Each time an auto-annotation is run there is a potential for a different result (just one additional gene call or non-call can throw off all the numbers). That is one of the reasons you always want your students to refer to genes by coordinates and not by gp#. We have the same issue - our genes are off by one number in Starterator reports. Not a big deal as long as students pay attention to start and stop co-ordinates Edited 30 Jan, 2016 16:11

Link to this post | posted 30 Jan, 2016 16:11

fogartym1

Lee Hughes
joyous726
We have something strange going on when we compare our auto-annotated Blast file in DNA master to what's in phamerator and starterator for ShiaLaBeouf_Draft. The gene product numbers/features don't align like they do for other phage genomes.

It is probably because the auto-annotations came up with different results (yours compared to the one done for the phamerator file). Each time an auto-annotation is run there is a potential for a different result (just one additional gene call or non-call can throw off all the numbers). That is one of the reasons you always want your students to refer to genes by coordinates and not by gp#.

We have the same issue - our genes are off by one number in Starterator reports. Not a big deal as long as students pay attention to start and stop co-ordinates

Edited 30 Jan, 2016 16:11

Posted in: Phamerator → Tutorial on Phamerator and Starterator Use?

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