Link to this post | posted 01 Mar, 2017 18:56

welkin

Hi Beckie— I love the Gordonia phages! These areas flanking the integrase seem particularly plastic and so it doesn't surprise me that the normal guidelines aren't holding up. Based on your GenemarkS output (which I think is the most compelling evidence you've got here) I want to keep the forwards 43 that is in the middle of that reverse operon. I also think you are right; you make sure that you call the reverse gene to start at 29163 and no longer to accommodate the forwards gene, and delete the other reverse gene that occupies the same space as the forwards gene. I could be persuaded to change my mind though, if you run them all through HHPred and find functions for the reverse gene that you propose to delete. -Welkin

Link to this post | posted 01 Mar, 2017 17:30

welkin

Hi Marisa, This is a great question. The NifU annotation came from our collaborators in Brazil, so Debbie and I weren't directly involved with the functional assignment in phage Barriga. I had to spend some time digging into "NifU" and what it does. NifU is a scaffold protein for Fe-S cluster complexes (not to be confused with the phage capsid scaffolding protein). It is frequently (but not always) involved in nitrogen fixation, as it is also found in species that do not fix nitrogen. The Barriga gene appears to align well with the NifU N , that is the N-terminal domain of NifU, but it is too short to contain both the N and C terminal domains of the protein. The N-terminal domain alone coordinates the binding of a single Fe while the C-terminal domain facilitates the binding to the rest of the Fe-S cluster. There are three Cys residues required for N-terminal Fe binding: Cys35, Cys62, and Cys106. A Smith-Waterman alignment places Barriga's cysteines in exactly the right place. So I think it is appropriate to add NifU-like protein (N-terminal domain) to our annotation list, and we should probably correct the others on phagesdb.org It would be interesting to see your phage has the C-terminal portion somewhere in a different gene. Here is the pubmed abstract on NifU, if you and your students are interested in further reading. https://www.ncbi.nlm.nih.gov/pubmed/10819462 Best, Welkin Edited 01 Mar, 2017 18:45

Link to this post | posted 26 Jan, 2017 14:48
welkin	What is the date and build is your installation? Look under "help –> about"

Link to this post | posted 25 Jan, 2017 16:14
welkin	It sounds like you are not running the program as an administrator. Right-click on the program icon before you launch the program and choose "run as administrator". Then try to import your .fasta file. Best, Welkin

Link to this post | posted 20 Jan, 2017 23:40

welkin

Hi Miriam, the red link is for his slipstream update for older versions of the program. The black link is the only link you should need. I am surprised that your program is running correctly if the executable is on your desktop. It needs to be physically located within in the DNA Master folder in the program files directory. This is why your student's version thinks it needs to download a bunch of supporting files via FTP— it is not in the right directory and it can't find its supporting files and databases.

Link to this post | posted 20 Jan, 2017 23:36
welkin	It should connect to Jeffrey's site automatically just by clicking the button.

Link to this post | posted 20 Jan, 2017 18:27

welkin

Hi Mary Ann, You shouldn't need the slipstream update. That was to update versions of the program from before 2012. The current version of the program that is installed when you download from JEffrey's website does not need the slip stream update. If you did somehow manage to get an old version, you would unpack that file in the C:\Program Files (x86)\DNA Master directory. His website was down a few times last week, which could have caused your FTP error. Have you tried again since then? Best, Welkin

Link to this post | posted 20 Jan, 2017 18:24
welkin	Hi Miriam, It looks like her database files are missing. Tell her to pick restore from FTP. IT should download everything she needs and then she should no longer get the the error.

Link to this post | posted 20 Jan, 2017 18:21

welkin

DNA Master runs just fine on Windows 10. It sounds like you are all running/rerunning the installer program, rather than actually running the DNA Master program. The installer is called dna master.exe while the actual program is DNAMas.exe (note the difference in capitalization and spelling). After you install, the actual program file will be found in the directory C:\Program Files(x86)\DNA Master. Make sure you launch the program by right clicking on the icon and selecting "run as administrator". Please let me know if that is not your case—and Miriam, I can't figure out your comment about the link at the end of the paragraph and the Desktop. But I am glad your is working. Best, Welkin

Link to this post | posted 18 Jan, 2017 17:02
welkin	Hi Tammy, Yes, the program is trying to interact with the servers at NCBI to run glimmer and genemark in order to populate the table. For a log, try the Event Manager, under Tools -> Database Managers. Best, Welkin