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Recent Activity

byrumc@cofc.edu posted in Classificiation with ICTV guidelines

Debbie Jacobs-Sera posted in Classificiation with ICTV guidelines

byrumc@cofc.edu posted in Classificiation with ICTV guidelines

Debbie Jacobs-Sera posted in Genome Comparison

Allison Johnson posted in Aca2-like protein

All posts created by debbie

Link to this post \| posted 28 May, 2025 15:01
debbie	Hi all, So if your file is live in GenBank, it will have the family classification stated there. You ca n use it. We could try to keep up as we enter things into GenBank, but honestly, ICTV can't keep up with us. Best, debbie

Posted in: General Message Board → Classificiation with ICTV guidelines

Link to this post \| posted 23 May, 2025 22:23
debbie	Kurt, This could be a bunch of things. My first guess is the actual files that you are comparing. Do the genomes open in DNA Master? It is likely a corrupt file I think. debbie

Posted in: DNA Master → Genome Comparison

Link to this post \| posted 16 May, 2025 17:51
debbie	Noe, look at line 65 in the approved function list (directly below the crossed out item). that hit is called a nuclease domain in the databases we use, but there is no nuclease function to that sequence. it is now named "ParB N-terminal-like domain" debbie

Posted in: Cluster C Annotation Tips → ParB-like nuclease domain

Link to this post \| posted 13 May, 2025 15:06
debbie	Chris and Maria, Excellent choices! Only call one. And do not call a wrap round version. debbie

Posted in: Functional Annotation → Help with Annotating Direct Terminal Repeats

Link to this post \| posted 06 May, 2025 17:36
debbie	Aurturo, Please use PineapplePizza as your prototype as to what to call each tail type in your pododvirus. I used P68 and phi29 as the prototypes to call that one. For genes 17 and 18 of Smelly (phamerator_draft), you can call both as minor tail proteins. Once you do that, If you have any questions, continue on the forum post. Thanks, debbie

Posted in: Functional Annotation → Potential minor tail proteins in cluster GK

Link to this post \| posted 05 May, 2025 15:19
debbie	Nikki, The data is coming fast and furious. For now, I would call these Hypothetical Proteins. but soon, we may have a better understanding. Best, debbie

Posted in: Functional Annotation → new HHPred hit to PDB 8JOU - Fiber I & fiber-tail-adaptor

Link to this post \| posted 01 May, 2025 23:28
debbie	Hi all, When annotating a Cluster O paper, please refer to this paper for help "Comparative Genomics of Cluster O Mycobacteriophages" https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725

Posted in: Cluster O Annotation Tips → Cluster O paper

Link to this post \| posted 01 May, 2025 23:19
debbie	Iain, Did you have a working DNA master? If not use this forum post to install. https://seaphages.org/forums/topic/5577/ If you did have a working copy, it has not been updated since Oct 24, 2021. The server where it sat is no more. So there is no need to update and you can't because the server is not available any more. We are working on it. The link above does work. debbie

Posted in: DNA Master → Issue uninstalling DNA Master

Link to this post \| posted 01 May, 2025 16:40
debbie	Arturo, Sure that will work. It would also be appropriate to call it a "endolysin, protease M15 domain". (I like this one better because it is less letters. debbie

Posted in: Functional Annotation → Two endolysins?

Link to this post \| posted 21 Apr, 2025 23:34
debbie	tRNA Scan SE may be back up, but it is still not showing the pictures. Please check the structure of the tRNAs if not available in tRNA Aragorn. Thanks, debbie

Posted in: Bioinformatic Tools and Analyses → tRNAscan-SE