Link to this post | posted 10 Oct, 2017 14:08
debbie	I asked the folks who are running the auto-annotations to check their settings. They have confirmed that they are using the same settings/versions. It is my understanding that Glimmer and GeneMark use a random 'sample' of the genome and to the best of my knowledge that explains the discrepancies. That explains why hand curation and the work we do with these genomes is so necessary.

Link to this post | posted 11 Sep, 2017 19:31

debbie

Recently, it was brought to my attention that the Wintermute lysate is contaminated. Upon investigation, it has been determined that Wintermute IS contaminated with Fionbharth. My apologies. Teachable moment: Whenever you receive a lysate, please always do the following: 1. Freeze the lysate for long term use. 2. Make a high titer lysate for your own use. Use preferred microbiology practice and make your phage lysate from a single plaque. PCR verify that plaque and your lysate. 3. Freeze aliquots of your high titer lysate for future use. debbie Edited 11 Sep, 2017 19:32

Link to this post | posted 18 Aug, 2017 17:56

debbie

Right now, you cannot auto-annotate in DNA Master. We are working at getting Glimmer and GeneMark onto servers to send DNA Master to. That should not be difficult but isn’t available yet. I'll keep you posted! If you are ready to auto-annotate now – I recommend using PECAAN. There are 2 ways to do it. Use the full suite of PECAAN functions and upload the files there. Once the genes are called, you can download a genbank file that uploads nicely into DNA Master. If you don’t want to use all of PECAAN, Claire Rinehart & Co. also created an auto-annotation tool that outputs the documentation of auto-annotation that can be pasted in the documentation window of newly created dnam5 file made from a FASTA input. (Claire commented on the difference between the 2: When the genome is loaded into PECAAN, the program will predict the genes but also do the BLAST for each gene. This can take some time and is system intensive. When the genome is loaded into the auto annotate tool, it only calls the gene and has less impact on our computing system. Therefore, if people don’t need the BLAST and HHPred results, please have them use the auto annotate tool.) IF YOU DO USE PECAAN, YOU CAN ONLY USE IT ONLY ONCE PER GENOME. So if you want the whole classroom to do this, use the auo-annotation tools for your students. If that doesn’t make sense, ask me again and I will explain. https://discover.kbrinsgd.org/evidence/summary https://discover.kbrinsgd.org/autoannotate/ It is quite the work-around, but it does get the job done. Edited 18 Aug, 2017 17:57

Link to this post | posted 02 Aug, 2017 14:51
debbie	There are multiple issues going on right now with servers. Chris Shaffer is right. The short answer for now is to auto-annotate in PECAAN and open the GenBank file it creates in DNA Master. (See Chris's message above.)

Link to this post | posted 19 Jul, 2017 21:16
debbie	When you cannot connect to the DNA Master server, you will get a false message that says you have the latest version of DNA Master. An error message of Glimmer failure is a strong indication that you do not have the DNA master update. I will have a work around tomorrow.

Link to this post | posted 31 May, 2017 15:35
debbie	Kayla, Great! Have you tried to phage hunt on your strain? debbie

Link to this post | posted 30 May, 2017 18:49
debbie	Hi Kayla, Thanks for the data. Do you have any interpretations? Did you repeat any of the infections? The ones that would be good to repeat are Tweety and Jeon. It might helpful to do full plates instead of spots. Do you know anything about the host you used? Thanks, debbie

Link to this post | posted 27 Apr, 2017 17:05

debbie

Nancy, I am not sure what you are asking. If you look at the phamerator map of the 3 genomes that you mention, it looks like these is a deletion in the G gene of the G/T frameshift in RitaG. That doesn't have anything to do with the frameshift. The deletion occurred and it looks like the phage can get along without that portion. That shouldn't stop you from calling the appropriate frame shift. I have included how I would call the frame shift in the attached document. if you are asking something else, let me know. Edited 27 Apr, 2017 17:05 117Kb 84Kb

Link to this post | posted 11 Apr, 2017 15:14

debbie

Susan, You can do the patch test on L-agar. Sure, why not! I don't understand the without top agar. the patch test is done to visualize phage release from a colony. So you need wild type smeg in the top agar for that detection. You make a companion plate with the patch test, so that your can carry that colony forward (without picking up WT smeg. does that make sense? You can always use a wire loop. Depending on numbers, that is a lot of firing the loop. You can also use sterile toothpicks for some of this testing.

Link to this post | posted 11 Apr, 2017 15:09
debbie	Nick, I will check with Claire as to what setting he uses. then we can see if they "match". i will keep you posted.