Link to this post | posted 23 Jun, 2020 23:18
debbie	Christos, I unpacked one of my files, so how your file was broken is extraordinary. My next advice is to revert to an older file that is not broke or to cut and paste from documentation. let me know if I can help. debbie

Link to this post | posted 23 Jun, 2020 14:55
debbie	Christos, I am still unsuccessful, but checking. Can you open and use a different .dnam5 file on your machine? Was PECAAN used to create your file? What is the next best version of your file? debbie

Link to this post | posted 18 Jun, 2020 12:51
debbie	Ok. Could you send me the file and let me try? I also couldn't fix a file recently, so I may need to get some help from Dr. Lawrence. Thanks, debbie

Link to this post | posted 12 Jun, 2020 11:21
debbie	Hi Christos, This how you fix the file. It is a bit tedious. https://seaphagesbioinformatics.helpdocsonline.com/article-104 Good luck, debbie

Link to this post | posted 02 Jun, 2020 17:03
debbie	JoAnn, I agree. The top hit is to HK97 gp 10. This phage is well studied by the Hendrix lab here at Pitt and while this is a structural protein in that phage, its function is unknown. The second hit is to a minor capsid protein. So it is easy to assume that this is a structural gene, which one is unknown. debbie Edited 02 Jun, 2020 17:04

Link to this post | posted 30 May, 2020 15:52
debbie	As you do a final check of your genomes, please review/compare the functions exported from PECAAN with the approved Functions List. Updates for both of these lists is a manual action, and not entirely synchronous. Edited 30 May, 2020 15:53

Link to this post | posted 30 May, 2020 15:50

debbie

Sigma factors and transcription factors are gene assignments that are use across all organisms. Gene regulation is everywhere! They are not unique to prokaryotes, and as such, they have diverse means in the context of, at the very least, prokaryotes vs eukaryotes. Today, May 30, 2020, we are going to avoid them all together and call such hits "DNA binding proteins" for now. One of the exceptions is WhiB. We will still call "WhiB family transcription factor" when appropriate. debbie

Link to this post | posted 30 May, 2020 15:37
debbie	Hi. After much deliberation, I believe that the best call for gene 60 (38695 - 39510 ) of Goose (and others) from Cluster A10 is to call it a "hydrolase". A very unsatisfying choice, but for now, we don't have enough information to identify a substrate that provides more information.

Link to this post | posted 22 May, 2020 00:20
debbie	Hi Sally, I am attaching my investigation for kicks and giggles. That this (or similar) is in other CZs and a P3 is fun! Punch line is that 39 can be called a toxin in a toxin/antitoxin system and 40 can be called an antitoxin in a toxin/antitoxin system. 1.78Mb

Link to this post | posted 21 May, 2020 00:45
debbie	Andy, I would still call this gene a Hypothetical Protein. Even though has hits to a thiamine binding domain, it is unclear what the function of it is. Considering how many hits it has to other things that have no identified function, it would be prudent to wait to call this anything.