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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
Link to this post | posted 30 Dec, 2020 20:04 | |
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Hi Matt, This sounds like 2 different problems, both alluding to incomplete download/installation problems. I would first recommend uninstall and reinstall. Also, does the installer have admin priviledges? You are missing some files/drivers. Do you still have DNA master on your old computer? We may have to do some copy/pasting. debbie |
Link to this post | posted 17 Dec, 2020 02:48 | |
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Dr. Catalase, Yes. Please use the validation function in DNA Master to do this when you renumber the genes. It is always best to let DNA Master auto-fill any field that you can debbie |
Link to this post | posted 15 Dec, 2020 21:24 | |
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Chris, You are the best! thanks, debbie |
Link to this post | posted 15 Dec, 2020 13:17 | |
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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 | |
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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 |
Link to this post | posted 09 Dec, 2020 01:35 | |
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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 | |
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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 | |
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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 | |
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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 | |
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Hi Amanda, I think you are right. I will get that corrected. Thanks, debbie |