SEA-PHAGES | All posts created by lhughes

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Link to this post \| posted 25 Feb, 2016 14:35
lhughes	I think you are going to need Dan's help to figure this one out. Lee

Posted in: Annotation → Locating Terminase Gene

Link to this post \| posted 24 Feb, 2016 22:26
lhughes	Hi Denise, I'm not a lot of help on this, but one thought that came to mind was locating the tapemeasure gene first and then working backward from there to the likely area for the terminase. Lee

Posted in: Annotation → Locating Terminase Gene

Link to this post \| posted 24 Feb, 2016 14:45
lhughes	jparker Hello, When we are compiling our final minimal annotation files for submission, should we leave the notes section for genes with no known function blank, or should we put "NKF"? Thanks! Jordan Leave those with no known function blank. Lee

Posted in: Notes and Final Files → NKFs in minimal files

Link to this post \| posted 18 Feb, 2016 19:36
lhughes	GregFrederick@letu.edu Thanks Lee. I had forgotten about that possibility. But does that mean that DaVinci (see image above) and all the others that do not have the programmed frameshift called are wrong and should be corrected? My guess would be that there is an error in DaVinci. That is one that should probably be reviewed. Which others (that aren't drafts) didn't have the frameshift annotated? Lee

Link to this post | posted 18 Feb, 2016 19:36

lhughes

GregFrederick@letu.edu
Thanks Lee. I had forgotten about that possibility. But does that mean that DaVinci (see image above) and all the others that do not have the programmed frameshift called are wrong and should be corrected?

My guess would be that there is an error in DaVinci. That is one that should probably be reviewed. Which others (that aren't drafts) didn't have the frameshift annotated?

Lee

Posted in: DNA Master → LO: Designation Question

Link to this post \| posted 18 Feb, 2016 16:42
lhughes	GregFrederick@letu.edu Look at feature 28. In Zaka and CLoudwang3 they apparently called the longest ORF. But based on guiding principles it does not seem "reasonable" because of the entire overlap with feature 27 in those two genomes. This one is easy to determine in our case because we have a STOP and this is the largest ORF in our case. But it obviously was not in Zaka and Cloudwang3. QUESTION: Do you want us to note those discrepancies so they can be edited? Are previous calls ever corrected/updated based on newer genomic information? Greg, I am going to suggest you have a look at the Annotation Guide section 9.4.1 in regard to your question about the feature 27 and 28 overlap you are seeing in Zaka and Cloudwang. This is a special situation. Lee

Link to this post | posted 18 Feb, 2016 16:42

lhughes

GregFrederick@letu.edu
Look at feature 28. In Zaka and CLoudwang3 they apparently called the longest ORF. But based on guiding principles it does not seem "reasonable" because of the entire overlap with feature 27 in those two genomes.

This one is easy to determine in our case because we have a STOP and this is the largest ORF in our case. But it obviously was not in Zaka and Cloudwang3. QUESTION: Do you want us to note those discrepancies so they can be edited? Are previous calls ever corrected/updated based on newer genomic information?

Greg,

I am going to suggest you have a look at the Annotation Guide section 9.4.1 in regard to your question about the feature 27 and 28 overlap you are seeing in Zaka and Cloudwang. This is a special situation.

Lee

Posted in: DNA Master → LO: Designation Question

Link to this post \| posted 08 Feb, 2016 21:43
lhughes	Did you just click the "Run as administrator" option on the icon, or did you actually change it to run as administrator under the "Advanced" tab for the icon properties? (Also depends on version of Windows. Windows 8 is different. I am talking about Windows 7 or 10.). Although it shouldn't make a difference, it actually does affect how the program works and updates when you don't have the icon set up correctly. Like I said, this is the most common reason I see this issue on student machines. Lee

Link to this post | posted 08 Feb, 2016 21:43

lhughes

Did you just click the "Run as administrator" option on the icon, or did you actually change it to run as administrator under the "Advanced" tab for the icon properties? (Also depends on version of Windows. Windows 8 is different. I am talking about Windows 7 or 10.).

Although it shouldn't make a difference, it actually does affect how the program works and updates when you don't have the icon set up correctly. Like I said, this is the most common reason I see this issue on student machines.

Lee

Posted in: DNA Master → DNA Master failed update

Link to this post \| posted 08 Feb, 2016 19:27
lhughes	In my experience, you should first check to make sure they are running the program as described in the Installation Guide (must be using a desktop icon that is set to "Run as Administrator" under the advanced button). That is typically the problem for my students.

Posted in: DNA Master → DNA Master failed update

Link to this post \| posted 08 Feb, 2016 14:57
lhughes	Thanks for the files, Chris! Lee

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 04 Feb, 2016 20:18
lhughes	Mojorita_Draft is failing on pham 18 of 59, pham 162. Tried all the standard things. Lee

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 02 Feb, 2016 19:22
lhughes	Dan - I have a student who wants to install the VM on his computer. Can I get the link please? Thanks, Lee

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

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