Link to this post | posted 14 Jun, 2018 21:19
debbie	The version is at help -> about. If you have not changed preferences to use secure servers, you will not get blast results. I have attached a picture of the correct settings. 160Kb

Link to this post | posted 13 Jun, 2018 12:39

debbie

Rick, This post should get your DNA master updated. debbie Dan Russell New as of November 15, 2016 Some very important changes have been made to DNA Master to accommodate NCBI's new secure https protocols. Versions of DNA Master from before this date will not be able to connect to NCBI and thus will not be able to auto-annotate genomes or run BLAST. Updating your DNA Master will allow you to be able to use NCBI's new protocols. See this blog post for more information. http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ –Dan Edited 13 Jun, 2018 12:41

Link to this post | posted 06 Jun, 2018 21:01
debbie	I think that the functional call for this particular instance could be nuclease.

Link to this post | posted 03 Jun, 2018 20:09
debbie	I think that we have missed a gene in these genomes. Look at the gap between upstream of the tape measure. I don't (yet) see the slippery sequence, but I think that is the T region of the G-T protein of a tail assembly chaperone.

Link to this post | posted 02 Jun, 2018 15:20
debbie	Sally, Hi. What gene are your questions about? The two functions together a DNA binding protein that sticks to the host membrane is more interesting than either a DNA binding protein or a membrane protein. I would call it as you have decided for now, but just curious. debbie

Link to this post | posted 30 May, 2018 00:52

debbie

I think that when I called this, I decided that thymidylate synthase is a generic enough term that it would be best until more is known. I unfortunately didn't put the more generic term "thymidylate synthase" on the approved list (until today). I didn't use dihydrofolate reductase because it wasn't on the list; it surely could be. Neither are very specific or satisfying, using both seems to be too much. We could add ThyA-like thymidylate synthase, but until someone wants to look at all thymidylate synthases more closely, I think it could be problematic. Chris - thank you for your investigation on this, it was very helpful.

Link to this post | posted 23 May, 2018 16:24
debbie	Unless of course there are 2 genes that have different domains that are part of a lysin (not unlike the Gordonia phages). That is the case in the Cluster AV genomes. The functional assignment for Jasmine gp 22 is best called as "lysin A, amidase domain"; while Jasmine gp 30 is best called as "lysin A, peptidase domain".

Link to this post | posted 27 Apr, 2018 02:28
debbie	Megan, I agree in your assessment. If I am right in the Golden annotation of the slippery sequence, then Adromedas shows a point mutation obliterating the slippage with a stop codon. While I believe that is where the slippage occurs, it is unclear how that works or what the slippage is. So I am confident calling both genes the TAC genes, but no slippage should be annotated.

Link to this post | posted 26 Apr, 2018 17:03
debbie	Thanks Welkin!

Link to this post | posted 26 Apr, 2018 12:06

debbie

Kayla, Hi. I have fixed the file. I believe the issue involves not providing DNA master enough time to build he database correctly. I used a DNA master utility to repack the file (which has no value until I show you what that means). I couldn't quickly find a protocol to this on the on-line bioinformatics guide. i will get it posted soon. If you are coming to the symposium/faculty meeting, let's chat. 1.39Mb