Link to this post | posted 21 Jun, 2018 21:56
debbie	Evan, GeneMark does call all starts ATG, GTG, and TTG (you will find that GenMark can agree with Glimmer on a TTG start in DNA Master). However, GeneMrk's graphic output is only coded to represent ATG (longer upticks) and TTG (shorter upticks) starts. I think they ran out of money to update all of the graphic displays…..

Link to this post | posted 21 Jun, 2018 16:24

debbie

Check out the genes upstream of the tail assembly chaperone (in Adaia, they are genes 8 and 9). it is easy to see that gene 8 is the major tail (HHPred results). Remember that it matches the SPP1 crystal structure project. This gene matches "H" which is a major tail protein and NOT the portal or head-to-tail connector complex protein. I am wondering if there is a legitimate programmed frameshift with this protein. See Baranov, et al 2006 where a major tail +1 ribosomal slippage is cited in a Listeria phage, PSA. While our slippery sequence doesn't match the one found in that major tail protein, our major tail protein - gp 8 - is 140 amino acids, while gp9 is 130 amino acids. A quick look at other major tail proteins across the actinobacteriophages, I have found gp sizes of 170 - 282 amino acids. Just wondering if the major tail protein is in 2 genes in this case. Further review is needed. Edited 21 Jun, 2018 16:27

Link to this post | posted 21 Jun, 2018 16:10
debbie	Be careful as you look for the second part of the tail assembly chaperone (T protein). It is a tiny bit of coding potential directly upstream of the tape measure that is not always called (only 1 in 3 have predicted it so far). All of them have same slippery sequence. refer to genome annotations of Adaia, Sputnik, and Atraxa for the exact calls.

Link to this post | posted 15 Jun, 2018 15:00

debbie

So you may be missing a driver. I am not sure. I have attached a picture of 3 files that should be in your DNA Master folder. Check the root of where these files are (captured in the attached photo) along with the 3 files that should be there. They are Windows files and don't move easily. I am providing one of them becuase it is the one that is usually missing. If you can't access this file from my DropBox, download it from the web. https://www.dropbox.com/s/uzlq44kn958fyma/msvcr100.dll?dl=0 37Kb

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.