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

Link to this post | posted 12 Jul, 2022 13:29
lhughes	Thanks for those insights, Chris. We haven't annotated a cluster BM phage yet, but I like how this case shows how important context can be when making these decisions.

Link to this post | posted 19 Nov, 2021 16:19
lhughes	Awesome! Thanks, Debbie. Lee

Link to this post | posted 19 Nov, 2021 14:52

lhughes

I'm getting the following error back from the Phamerator import process for SEA_TOMAS_193 (Tomas_TRNA_40): "ERROR: Evaluation ID: TRNA-EVAL-018. Status: error. Definition: Check if the tRNA coordinates appear to match the Aragorn or tRNAscan-SE prediction(s) for SEA_TOMAS_193 (Tomas_TRNA_40). The tRNA feature is expected to have coordinates that match Aragorn or tRNAscan-SE. Result: The tRNA coordinates (99205, 99279) appear to be incorrect. Left coordinate looks correct. Right coordinate should be moved left by 3 base(s). Status was changed from 'warning' to 'error' automatically due to no interactivity." This tRNA does not show in the web-based Aragorn output. It has an infernal score of 38 in tRNA-Scan. When I check the DNA Master file, the coordinates are different (99206-99279) so am confused by the message saying the left coordinate is correct (the message has a different number than my file) and that makes me question exactly what coordinate is meant by the suggestion to move the right coordinate to the left by 3. (In looking at this, I note that moving the coordinate left by one would leave a "CC" as the last two bases of the tRNA, which would seem to be in keeping with what would likely be expected based on the diagrams in the guide.) I'm attaching a screenshot of the current call in the context of the genome sequence. Suggestions on getting this right so it will import into Phamerator? Lee 263Kb