Link to this post | posted 05 Jan, 2021 14:10
debbie	Fernando, There are a lot of factors that impact how poorly Blast completes. It sounds like it just needs to have more time. I have waited longer than overnight to complete a blast. You can try blasting in sections. See this section of the guide. https://seaphagesbioinformatics.helpdocsonline.com/article-70 good luck! debbie

Link to this post | posted 30 Dec, 2020 23:44
debbie	Matt, Ok. It is never simple, is it? Good luck. debbie

Link to this post | posted 30 Dec, 2020 20:04
debbie	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
debbie	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
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