Link to this post | posted 13 Jan, 2022 16:52
powelleann	My class is using DNA Master to annotate our first genome this semester. I noticed that we no longer need to enter notes in the specified format in the notes area of DNA Master. Is there a spreadsheet format or file type that you would like us to use? Please let me know. Thanks.

Link to this post | posted 13 Jan, 2022 17:15

debbie

Hi Ann, In the words of Eeyore "Thanks for noticing!" The new direction is meant to make your decision making on your gene calling as simple as possible and as meaningful as possible. In addition, the notes were not very helpful in the QC process. I have modified 2 pages to help as you construct the notes that will work for you. https://seaphagesbioinformatics.helpdocsonline.com/article-44 https://seaphagesbioinformatics.helpdocsonline.com/officialdocumentation I am hoping that this post today will encourage others to upload "Here's what I use." The goal of this notes record is to provide the evidence needed to get annotations improved so that when you are done, they are really ready to go directly into GenBank. So asking for help or review along the way is encouraged. If you wish to use the same format for notes as before, that will be acceptable for now. Let me know if you have any questions. debbie

Link to this post | posted 13 Jan, 2022 18:04
kbutela	We use this attached spreadsheet for students to document their notes and conclusions during the annotation process. 102Kb

Link to this post | posted 13 Jan, 2022 18:08
kbutela	When students finish annotation their genomes, we use this spreadsheet to track their changes. They document which genes were changed and rationale for functions. We then have students peer review each other's original annotation spreadsheets and document their reviews in this spreadsheet. I could see modifying this review document as a summary of your notes for the genome you annotated. 25Kb

Link to this post | posted 13 Jan, 2022 18:29
powelleann	Thank you so much for the information.

Link to this post | posted 13 Jan, 2022 19:20
jawsWPI	For those who use PECAAN. Attached is the notes template (excel file) that my students will be using, and the instruction document. In the first round each student will annotate an assigned coordinate range. In the second round they will peer review (as Kristen's students do) a different range with access to the first round notes. Edited 13 Jan, 2022 19:21 8Kb 15Kb

Link to this post | posted 13 Jan, 2022 22:07

MSMC

jawsWPI For those who use PECAAN. Attached is the notes template (excel file) that my students will be using, and the instruction document. In the first round each student will annotate an assigned coordinate range. In the second round they will peer review (as Kristen's students do) a different range with access to the first round notes. We do something very similar with peer review, using a Google Doc for students to record their annotation data.

Link to this post | posted 14 Jan, 2022 22:05

kmaclea

I'm still a little unsure how to turn this into Notes that QC reviewers downstream can use once we submit our genomes. Are we suggesting that one will submit the DNA Master Minimal File, and then an attached Spreadsheet or linked Google Doc that has info on each gene, which will then be reviewed alongside the Minimal File by the QC reviewer? And that the files in question do not have to follow any particular format? So some schools may submit much larger files than others? Are there guidelines on length or what is included (screenshots, etc.)–because a spreadsheet can compactly give certain info, but a Google Doc with inserted screenshots, etc., would be very different. Thoughts from anyone? Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 14 Jan, 2022 22:20

kmaclea

I'm still a little unsure how to turn this into Notes that QC reviewers downstream can use once we submit our genomes. Are we suggesting that one will submit the DNA Master Minimal File, and then an attached Spreadsheet or linked Google Doc that has info on each gene, which will then be reviewed alongside the Minimal File by the QC reviewer? And that the files in question do not have to follow any particular format? So some schools may submit much larger files than others? Are there guidelines on length or what is included (screenshots, etc.)–because a spreadsheet can compactly give certain info, but a Google Doc with inserted screenshots, etc., would be very different. Thoughts from anyone? Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 14 Jan, 2022 22:44

debbie

Hi Kyle, The simple answer to you questions and assumptions is yes! The SMART Team is pretty smart and I think they will be able to follow whatever you provide. The purpose of these notes is 2-fold. One is help get to best answer in the genome review process. If you get to the best answer, they don't have to spend a lot of time in your notes. But, if they find the annotation lacking, the documentation of how you made the calls can help them. The second is to help you - the annotator - document your gene calls so that we can help where needed. We can't help you and you can't help you if you can't see the rationale of what you did. Don't over think this, make your notes meaningful and it will all work out. Check out the links posted above for more of the rationale. Sounds scary, but should simply. debbie