Link to this post | posted 15 Dec, 2020 21:24
debbie	Chris, You are the best! thanks, debbie

Link to this post | posted 15 Dec, 2020 13:17
debbie	Juan, GpXX is incorrect. You should use the buttons of DNA Master to overwrite gpXX with Hypothetical Protein. The function field is empty. The Bioinformatic guide should be followed. CDS 379 - 1161 /gene="1" /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" Good luck! debbie

Link to this post | posted 09 Dec, 2020 01:38
debbie	Hi all, 3 of EK1 genomes (CrunchyBoi, PineapplePluto, and Pabst) have a wrap around gene at the end of the genome. See forum post https://seaphages.org/forums/topic/5138/?page=1#post-8394 Edited 09 Dec, 2020 01:39

Link to this post | posted 09 Dec, 2020 01:35

debbie

Kirk, I'll weigh in. I like the way you are thinking, I would call this gene. Easily if it were in the middle somewhere; with trepidation that it is at the end of the genome. None of our commonly used programs 'like' genes that wrap around the end of the genome. GenBank consistently asks us if that is a really thing because we report a 'linear' genome with a gene that wraps around the ends. It is difficult to grasp that a phage genome circularizes, go figure! Phamerator is also not able to easily display a wrap around gene. If you look carefully at genome with an end-wrap around gene (like in some of the cluster C1 genomes), you will find what looks like a vertical random number displayed on a phamerator map at the midpoint of the genome. So while it is a great find, it is very unsatisfying to see it displayed. I want to link this to the cluster specific tips forums, because it may be the only place where this gene is celebrated. As a footnote, when identifying base 1 of a circularly permuted genome I try very hard to find a gap, so i don't do this. Darn if the biology didn't catch me. Curious what others might think about it all. Thanks! debbie

Link to this post | posted 04 Dec, 2020 12:45
debbie	Hi Kirk (and all), The fix will be posted on Monday, December 7, 2020. debbie

Link to this post | posted 03 Dec, 2020 04:05
debbie	Hi Kirk, I can verify the same results that you obtained. I have sent an email to Jeffrey. I'll keep you posted. debbie

Link to this post | posted 19 Nov, 2020 06:24
debbie	Hi WUSTL, I have added "NAD-dependent deacetylase" to the list of approved functions! Thanks for identifying it! debbie

Link to this post | posted 17 Nov, 2020 11:34
debbie	Hi Amanda, I think you are right. I will get that corrected. Thanks, debbie

Link to this post | posted 11 Nov, 2020 20:57

debbie

Hi Christina and Nikki, I think I would first rely on the coding potential and call the longer version of 71. While I would likely fill in this space with genes of the 4 bp overlap variety when I didn't have compelling coding potential choices, i like the coding potential better here. While this may not help (but I haven't looked lately), there is a paper with mass spec for the genes of some of the Cluster J phages. I am sure if we had evidence of the 2 genes for the phages in that paper, we would have called them. From my quick glance, we did not. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273 debbie

Link to this post | posted 07 Nov, 2020 18:50

debbie

To fix a "Key Violation" error, this should work: Make yourself a backup directory on your desktop (name it something like OldRecentFiles) Then browse to C:/ProgramFiles/DNA Master/DMDB There will be a bunch of files in there that all start with "RecentFile" Move all of those into the new backup directory on your Desktop just in case. Then restart DNA Master. It will say that it can't find the RecentFile DB files, and will download new copies of them (this should happen automatically). If not, click the button marked "Download from FTP site" at the upper right hand corner of the table that pops up. You can then discard the files that you moved out.