The following description are my notes on how to export PECAAN annotations and import the information into DNA Master. Enjoy!

Export PECAAN files
In PECAAN, go to the Export menu and click on the “Export CDS Function” button to export the PECAAN file into a .txt file that can be opened in BBEdit or any other pure text editor. When the PHAGENAME is displayed, put SEA_ before the PHAGENAME, if the phage is from the Science Education Alliance (SEA) program, otherwise just continue.

Create DNA Master file with PECAAN annotations
When starting DNA Master choose the center option to import a .fasta file and auto-annotate. Navigate to the phagename.fasta file, when the popup window asks for the .fasta file, and click on it. When the Annotate window is displayed, select the options that you want and click the “Annotate” button. When auto-annotation is complete, close the log and message windows. You now have a DNA Master file.

To import the PECAAN annotations, click on the “Documentation” menu option. Open the PECAAN Phagename_cdsfunctions.txt file in a text editor, such as BBEdit. Click on the annotation text, go to the “Edit” menu and click the “Select All” option and then the “Copy” option from the same menu. Go back to the DNA Master “Documentation” window and right click on the text. Choose the “Select All” option from the popup window. Right click again on the text again and choose the “Paste” option. This should replace the auto-annotation documentation with the PECAAN documentation. Next click the “Parse” button in the upper right corner of the DNA Master Documentation window. Select the first five features on the left of the pop-up window and select the “Bacterial and Plant Plastid Code” option for the “Genetic Code” option. Pres the “Parse” button.
Go back to the Features menu window and continue with the preparation of the GenBank file.
In the Features window, right-click on the Name header and select the Wide Feature List option. You should see the Tag as SEA_PHAGENAME_#. Prepending the SEA_ tag to the PHAGENAME was an option in the PECAAN “Export CDS Function”. If you do not see this format then in the validate window, described next, you will need to check the “Override” button at the bottom the “Validation” window and put SEA_PHAGENAME into the “Locus Tag Prefix” and press the “Reassign Gene Data” button.
Go click the Validate button at the bottom of the gene list window. You get an all clear for the starts and stops. You may see a note about the two tail assembly chaperone genes sharing a 5’ start. That is OK if there is a frame-shifted gene in your genome and these stop sites correspond to those genes. If there are any other error notes, go fix them and then re-validate until the errors are resolved. If the Tag column is in the SEA_PHAGENAME format then you are done with the validation, if not, then look at the previous paragraph for instructions. When finished, click on the Description button to see the Product, Function, and Notes fields.
Save the DNA Master file as PhageName.dnam5 in the phage folder with the .fasta and author files.
If coming from PECAAN’s “Export CDS Function”, PECAAN export has already put the functions from the notes into the Product field, populated the NKFs as “hypothetical proteins” and if prepended the phage name with SEA_ then the tags are properly set. Scroll through a few genes to verify that this has been done by looking for “hypothetical protein” in the Product field for those genes without a function, i.e., NKF in PECAAN.