Link to this post | posted 23 Mar, 2017 23:50

debbie

I am going to add to Chris' correct statement. The "functional annotation" does eventually get put in the product field - by SMART. But you are asked to place functions in the notes. There are buttons in DNA Mater that move the contents of the Notes, Functions, and Products fields. We ask for it in the Notes so that as we overwrite the final file, it will format correctly. So your thinking is logical, our protocol is simply a logistics request to minimize the amount of re-formatting done at QC.

Link to this post | posted 13 Mar, 2017 15:39
debbie	Kayla, I use big plates - 150 x 15mm. You can do fewer lysates/plate if you want to use the 100 x 15mm. Whatever you have available is great! Thanks, debbie

Link to this post | posted 03 Mar, 2017 16:54

debbie

Victoria, Mass spec data of a few of these instances shows the protein starting at the amino acid next to the second start. Since it is common that the first methionine gets chopped of in post-translation processing, that NO methionine is present in the mass spec reads, it is likely that the second methionine initiated translation. So in this example, the 4 bp overlap gets 'trumped'. This decision is based on the simplest possible answer. and never forget, things do not have to be simple!

Link to this post | posted 11 Feb, 2017 16:39
debbie	Vassie and Lee, Happy visiting! You can post your results on this forum under the topic "Post Results Here". I also provided a format, so that the results reporting could be consistent. The same procedure is in place at the Xeno Challenge Forum for those results. I am curious to see if these mechanisms work, so by all means, post away! Thanks! Edited 11 Feb, 2017 16:40

Link to this post | posted 26 Jan, 2017 18:37

debbie

I am prefacing this with what I think is happening, but I could be misdiagnosing. It looks like your DNA Master folder is on your desktop, but the program is looking for files in the program files folder. You have two ways to go forward. 1. Put your DNA Master folder back in program files (or re-download to there). Then, shortcut the .exe program (but not the installer) to your desktop. 2. Change all of the paths (in directories) to where you have put the appropriate folders. I would recommend #1.

Link to this post | posted 25 Jan, 2017 16:45

debbie

Persistent Glimmer Failure Remedies Glimmer failures during auto-annotation are most likely due to an ability for that computer to connect to NCBI (where Glimmer resides). Possible explanations are: 1. The Glimmer site is down. But since some computers connect, that is unlikely. 2. The program is not updated. This is difficult to tell because if when the update button is pushed and the program could not connect to the DNA Master website, the response message is “this version is up-to-date”. Do not assume that if you receive this message, your program is up-to-date. To clarify, check the build number, it must be Version 5.23.1 Build2490 03 Dec 2016. (To check go to Help -> About) 3. It could be that the server (ncbi) got too many requests at the same time, so not all connected. Which means “try again”.

Link to this post | posted 17 Jan, 2017 22:11
debbie	Hi. I sent your question to Dr. Lawrence, the author of DNA Master. He suggested that "Looks like the database did not install. Likely a permissions problem in that they cannot open those tables because you need administrator access." Are you sure you are running the program as an administrator?

Link to this post | posted 04 Jan, 2017 18:06
debbie	Here is the list of phages for the host range project and their titers. Note: Wintermute is a phage found by Bryan Pasqualucci at Southern Connecticut State University (incorrectly labeled in the sheet that was sent with the lysates). Sorry Bryan! 20Kb

Link to this post | posted 03 Jan, 2017 16:33
debbie	Roy, Happy New Year! I sent an email to Dr. Lawrence and he rebooted his website this AM. I found it to be working now. Thanks for the heads up, debbie

Link to this post | posted 16 Dec, 2016 20:33

debbie

PECAAN (Phage Evidence Collection and Annotation Network) Claire Rinehart, from Western Kentucky University, introduced us to PECAAN at last summer’s Retreat. PECAAN is a companion program to DNA Master (not a replacement), streamlining the complicated decision-making process of Gene Prediction by displaying relevant evidence for each gene on its own web page. It also provides a record-keeping system that can be used as input to create your final DNA Master files. Using PECAAN is optional. You may want to add PECAAN into your students’ workflow once they get the hang of using DNA Master and evaluating the data from the various data sources. Or you may want to use it as a tool for the final review of your genomes because it stores BLAST (PhagesDB and NCBI), HHPRED, and Starterator data for the entire genome and can output this data into DNA Master as a functional file or as a fully annotated file. To gain access to PECAAN, instructors should email claire.rinehart@wku.edu a request along with:     Firstname, MI, Lastname     Email     Full institution name     Approximate number of students in their group. The PECAAN user manual is available on seaphages.org on the Faculty Information page. The user manual contains instructions on how to load phages into PECAAN and how to add your students as users of the site. Edited 16 Dec, 2016 20:34