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Using PECAAN in class

| posted 26 Jan, 2018 19:46
I posted this question elsewhere. But I will put it here as well since you all are having an active discussion.

Some of the Notes section documentation changed in the new online Bioinformatics Guide. There are several codes which changed and some that are new.

Those that I remember off the top of my head are:

SD: changed to RBS:
CIF Blast:, CIF HHPred, and CIF Synteny are new this year IIRC.

QUESTION: Has the PECAAN output for DNAM5 been updated with these new notes documentation requirements?
| posted 28 Jan, 2018 01:48
Steve,
The PECAAN User Guide can be found at:

https://seaphages.org/media/docs/PECAAN_User_Guide_Dec7_2016.pdf

-enjoy!

Claire
| posted 28 Jan, 2018 01:50
Greg,
We are aware of the DNA Master changes and we are working on bringing PECAAN exports to DNA Master into alignment with the new format. It is not there yet. I will post here when we finish the update.
Thanks,
Claire
| posted 28 Jan, 2018 22:12
Super! Thanks Claire! We appreciate your hard work.
| posted 16 Apr, 2018 02:35
The PECAAN export is pretty close to what is needed for the new DNA Master notes format. If anything, the annotation notes may be a little detailed but it is easier to edit by deletion than to enter notes by hand.

-Enjoy!
Claire
| posted 08 Feb, 2019 14:49
This thread has been quiet for a little while, but I wanted to get some advice from people using PECAAN in class. This is the first year we are using PECAAN in class (so far, so good).

The only functionality that I can't seem to utilize in PECAAN that is in DNA Master is to investigate gaps for potential genes. In DNA Master, you can highlight the ORF, insert the gene and then BLAST the translated protein. I was trying to insert a gene in PECAAN to do the same thing, but the way it is formatted on the browser prevents me from putting in the information on the top of the box - it is obscured by the banner with the drop down bar and button for "Host-Trained GeneMark" (I'm attaching a screenshot). I have this issue in both Chrome and Firefox. Has anyone else run into this?
| posted 08 Feb, 2019 18:01
Setting the zoom level to 100% is always the first thing I have students try, it usually resolves the issue.

I.e. change this setting to 100%:
| posted 08 Feb, 2019 19:46
cdshaffer
Setting the zoom level to 100% is always the first thing I have students try, it usually resolves the issue.

I.e. change this setting to 100%:

Thanks Chris. Is there a way to change the zoom on one portion of the browser? If I change the zoom doing a Command+ or Command-, the entire window gets larger or smaller, but the ability to see the box for putting the gene information doesn't change.
| posted 11 Feb, 2019 16:06
Yeah, the change in zoom level does not always work, which is why I said "first thing to try". The difficulty is that different browsers and different systems make it so there is not one solution. You can also try just scrolling up or down, it works on my mac if I use the scroll wheel on my mouse but you have to have a mouse with a scroll wheel. Also try scrolling down a little before you click the add gene button so you have room to scroll back up to get to the top. Also on my mac at least, the window opens with the curser active in the text box, so I can click the add gene button and just start typing and the window will auto-scroll so I can see the text box.
| posted 14 Feb, 2019 16:34
cdshaffer
Yeah, the change in zoom level does not always work, which is why I said "first thing to try". The difficulty is that different browsers and different systems make it so there is not one solution. You can also try just scrolling up or down, it works on my mac if I use the scroll wheel on my mouse but you have to have a mouse with a scroll wheel. Also try scrolling down a little before you click the add gene button so you have room to scroll back up to get to the top. Also on my mac at least, the window opens with the curser active in the text box, so I can click the add gene button and just start typing and the window will auto-scroll so I can see the text box.

Thanks Chris. It turns out when I scroll down, then "Add Gene", it works. All is well.
 
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