Link to this post | posted 03 Apr, 2024 13:47
lhughes	It opened fine for me just now. Lee

Link to this post | posted 06 Feb, 2024 16:44

lhughes

Hi Adam and Debbie, I did a very quick look at this yesterday. There are 32 phages in BD2, but only 13 had this particular gene call based on Phamerator data (and 3 of those, including Superstar are draft annotations). I only did a quick glance through them and didn't see a clear pattern on the overlap sizes that have been called, but I didn't really have a chance to look into them in detail. Please continue to share your progress here. We are annotating the two other draft genomes at UNT right now. Thanks, Lee

Link to this post | posted 26 Jan, 2024 14:51
lhughes	Fred - my understanding is that each program determines how to label the different frames independently, so there is no "standard" for which is going to be -1, etc. You need to determine which aligns with which each time you compare the data from two different programs to make sure you are comparing apples to apples. Lee

Link to this post | posted 12 Jan, 2024 21:09
lhughes	Congratulations on your retirement, David! It has been wonderful to have the opportunity to interact with you as the SEA has grown. Thank you for all you have done to help make this possible. All the best, Lee Hughes

Link to this post | posted 12 Jun, 2023 13:39
lhughes	Hi Steve, If you can't get the DNAM workaround from Kristen to work for your class, I'm happy to share how we use PECAAN in our classes (slides and other resources). We use PECAAN first in our annotation classes. Lee

Link to this post | posted 07 Jun, 2023 16:53
lhughes	Kathleen, Did you ever get an answer to this question? We just got sequence back on a new BM and will be annotating it in the near future, so I am interested in what you found out. If you haven't gotten an answer yet, it might be worth emailing Chris Shaffer for more information. Lee

Link to this post | posted 09 May, 2023 13:46
lhughes	Thanks, Debbie. Good to know it's not just me, and thanks for the thoughts on a workaround. Lee

Link to this post | posted 08 May, 2023 21:00

lhughes

I have been getting errors when trying to download some genomes from GenBank, but not all. I'm attaching an image of the error I received today trying to download Streptomyces phage Andris. I'm not sure if this is part of the problem or not, but all the genomes that have given me this error have been more recent (I've verified that they are active in GenBank) and seemed to have an accession number starting with the letter "O". Lee 87Kb

Link to this post | posted 19 Apr, 2023 20:31
lhughes	Thanks, Debbie. I noticed all of our (UNT) more recent genomes that have a member of this Pham have used the "phosphatase" function so that makes the most sense given that we would need more evidence in order to call the more specific function. Lee

Link to this post | posted 18 Apr, 2023 14:08
lhughes	Can I add a wrinkle to your question (I also have a phage that we are currently annotating that has a member of this Phamily)? In the Official Functions list it gives ClubL144 as the example for the 5'nucleotidase function but when I look it up on PhagesDB that gene has a function of "phosphatase" showing on the Pham page. Lee