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Using PECAAN in class

| posted 18 Dec, 2017 16:52
I am curious as to whether schools are having students annotate using PECAAN in addition to / or in replacement of having them reach out to each of the sites separately (phamerator, starterator HHpred etc.)
| posted 09 Jan, 2018 20:05
We are using PECAAN in lieu of pulling from each site separately mainly because the check marked annotation evidence is always live and readily available for other students to view and use in correcting annotations. All changes are recorded in a change log so it is easy to see how the annotation has evolved during the course of discussion on a gene and the evidence is right there to validate the annotation. We found that PECAAN saves hours and hours in the confirmation and checking process since all of the data is always at your fingertips. The BLAST, HHpred, conserved domain and TMHMM data are essentially what you get when you pull the information directly from the network sources. There are dates at the top of each data section indicating when the data was pulled from the network. If you want to get more recent hits then a button is available at the top of each data section that allows you to update the gene data (which only takes a few minutes).
We found that after a few class periods for introduction and working on an example genome, the students are able to jump right into their genomes and typically they are finished after six two-hour labs. Using the DNA Master approach it would take the whole semester to do a genome with six people. Now, we sometimes offer the option of doing a second genome, especially since sequencing costs have gone down so that we can usually sequence 8 or 10 additional phages per class.

For disclosure purposes, we created PECAAN so we are really sold on it.
| posted 09 Jan, 2018 21:29
We also use PECAAN as our primary source of information that is used by our students. As well, we encourage them to go directly to the data sources when graphical output would better inform them. We have found that annotation goes much more quickly using PECAAN, since the time spent waiting for data to run is so much less. I think it is a great tool!

| posted 10 Jan, 2018 19:10
I checked out PECAAN, but didn't really spend any time with it. Let me ask a quick question, does it require that a Starterator file is uploaded to run? I wasn't sure, and tried it on a phage that was in phamerator and already annotated (but without starterator), and the system just spun it's wheels. I am wondering if that's why.

| posted 11 Jan, 2018 16:35
PECAAN did, at one time, require that Starterator files be attached during setup of the sequence. Chris Schaffer has now posted Starterator reports for each pham and so now we simply keep the Pham information in PECAAN and link to Chris' excellent Starterator reports directly so that they display in a tab in PECAAN. Chris updates these reports as Phemerator is modified so that all of the information from Phamerator, Starterator and PECAAN are synced. Good stuff! Give it another try.

| posted 11 Jan, 2018 21:35
We have introduced PECAAN to the students this first week of class and are excited to use it as the main source of information, as well as showing the students where the information was originally collected from.
At first I thought that PECAAN was too good to be true and that we would still need to access each resource separately - PECAAN really helps to streamline the annotation so much! I would also like to say that the help guide going along with PECAAN is extremely user friendly (as is the new online bioinformatics annotation guide).

Thanks for sharing the resourcesmile
| posted 11 Jan, 2018 21:59
Last year, we did both traditional annotation AND we introduced PECAAN. We wanted them to learn the traditional way first, so that they would better understand what to look for in PECAAN, and to really grasp what all the evidence pieces mean. While annotating with PECAAN was preferred by the students (and did go WAY faster), our students often missed important considerations (like exploring gaps) or failed to check/uncheck boxes, thus making errors in their annotation. Perhaps with a bit more practice in teaching them how to use the tool (and increasing the number of students looking independently at each gene) we would have more success. This year, however, we are going back to the traditional method; among other things, we find having the graphical representations really helps the students to make better calls.
| posted 11 Jan, 2018 22:22
We had similar problems with missed genes and so we added a Pham Maps menu to PECAAN that allows you to pop up the phamerator style map in a separate window or tab (with right click). This has helped so much that I do all of my annotation and checking with a separate Pham Map window being displayed along side my gene window. Pham Maps lets you select (from a drop-down box) another phage from within the same cluster and it is displayed underneath your current phage map. The color of the genes are the Phamerator colors and it is easy to see at a glance the conservation of gene order between the two displayed genomes even though they may be shifted relative to one another. You can confirm pham membership by moving the mouse over a gene which then displays the pham, start/stop and function (if available). The real advantage is that you can easily change the phage that you are comparing so that as you move through the genome and your BLAST results begin to hit other phages, you can easily change your Pham Map phage. In some clusters it is an easy way to display the mosaicism of phages as you move along the genome. Finally, as you make changes in your genes in the main PECAAN window, the Pham Map display is updated when you refresh the Pham Map window.
Give it a try!
Edited 11 Jan, 2018 22:27
| posted 11 Jan, 2018 22:37
Ooh! This does sound like it would be very helpful! Thanks!
| posted 19 Jan, 2018 17:24

I did just try PECAAN again, and you are exactly right, it loaded perfectly. Now, a second question. It's been so long since I looked at it, I don't know where everything is. Where can I find the user guide you all are referencing, or even a tutorial if you have one for students?


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