Link to this post | posted 11 Feb, 2025 17:38
debbie	Hi Olga, Technically there is no difference. However, "Hypothetical Protein" is the only acceptable choice. debbie

Link to this post | posted 08 Feb, 2025 15:39

debbie

Hi Kristen, I will send you to the literature for this. When Dr. Lawrence adopted this method of SD determinations, he used the work of Dennis Kibler and Sam Karlin. I was under the impression that the spacer distance was between the end of the Shine DalGarno sequence and the start. Since SD sequence rarely match the lambda sequence, and the non-perfect matches have weighting schemes, i don't know how to count. the manual has a Kibler reference and here is a Karlin reference. Go to the preference settings of DNA master and note that we have picked Kibler 6 and Karlin medium (quite arbitrarily). But the matrixes provided are quite involved. Other questions: The Z score uses the final score. But note that both numbers reflect similar relationships. "Karlin Medium Shine-Dalgarno spacer matrix in the local settings of DNA Master" - the DNA Master setting (if you are using the most updated DNA Master are Karlin-Medium scores (unless you change your settings in the preferences. Remember, both Kibler and Karlin are applying math to a 'best fit' situation. some may not be easy to recognize. And sometimes a SD sequence is not even in play, so that the numbers are quite useless. Let me know if you want to chat more about this. best, debbie

Link to this post | posted 06 Feb, 2025 18:04
debbie	Hi Holly, I recommend that you follow Sally's advice and call it an "ASCE ATPase". Thanks! debbie

Link to this post | posted 05 Feb, 2025 19:45
debbie	Hi Sean, Yep. we have seen many examples of DNA Master not returning blast results for a few genes (even when every other gene in a genome blasts just fine). Just make a notation that blast results for those genes wouldn't save. We appreciate that you reBLASTed! You can move forward with your submission. best, debbie

Link to this post | posted 04 Feb, 2025 05:02
debbie	Are you sure that you want to uninstall? If you are clicking on DNAMaster.exe instead of DNAMas.exe you will be asked to uninstall. You do not want to do that. DNAMaster.exe is the installation program, but DNAMas.exe is the program. Once downloaded, you can delete the DNAMaster.exe file. Carefully follow to the installation guide on phagesDB. Let me know if that helps. debbie

Link to this post | posted 04 Feb, 2025 01:28

debbie

Hi Arturo, It is an orpham, but that is ok. Better than ok. You are working on a phage that is the second member of cluster. So careful, de novo inspection (meaning, don't rely on what was called in the first genome, but make your best calls that you can yourselves.) and then enjoy when you come to same conclusions for same/similar genes and celebrate when you find a gene - like this one – that no other genome in our database has! (Remember to blastN it!). And i would call it a membrane protein

Link to this post | posted 04 Feb, 2025 01:13
debbie	That would be great!

Link to this post | posted 03 Feb, 2025 21:34

debbie

Hi Levi, When you enter your phage, give it an additional notation like, QuinnAvery_UDM. and yes, please delete when you are done. Department computers can be really good, because once they are set up, they are good to go! OR they can be problematic because IT wipes all machines clean every night. Please try to stick with that on your end (not as a class item), and get IT to see what needs to be done to get this working. It is worth the time. best, debbie

Link to this post | posted 28 Jan, 2025 21:19
debbie	You can install in a different place (like your desktop) and see if that works, then delete the old stuff.

Link to this post | posted 28 Jan, 2025 21:08
debbie	Hi Levi, I am not sure I have ever seen this. Did you just try deleting it? If you are installing it in a different location, it may not matter. best, debbie