Converting a Serial Cloner sequence to Unipro UGENE

This describes how to take a Serial Cloner sequence with annotated features and move it into Unipro UGENE with your favorite text editor and minimal effort. The annotated features from Serial Cloner will ultimately be intact and displayed in UGENE if you follow this process. The process of going from Serial Cloner to UGENE seems much simpler as the feature annotations in UGENE display by default.

Main thing is you need a GenBank-formatted file generated from Serial Cloner. You can open that file in UGENE.

Step 1: locate the Serial Cloner file and generate the Genbank files you'll need

If you haven't done so already, you'll need to convert from the Serial Cloner file format that ends in extension .xdna to the Genbank format.

  • Find your Serial Cloner file ending in .xdna and open it.

  • Under File > Export > Export As GenBank and save, preferably with a distinguishing name. (It will have a .gb extension but you may not see this depending on your system's view settings for extenstions.)

Step 2: Save as UGENE project or document format and clean up

  • Save the file so you can open it in UGENE later without needing to repeat the conversion. I prefer to save each sequence I work on as a separate UGENE project, but you can choose whatever approach works for you work style. It is advised that you save it in a manner to clearly distinguishable from the SERIAL CLONER files, optionally even in a separate folder. For my approach, I use File > Export Project, give it a good name, and save the project in a new directory.

  • At this point, you can delete the Genbank-formatted file generated by Serial Cloner. This is probably best as the UGENE project will have a Genbank-formatted file in the project folder and it could become confusing. Either Genbank-formatted file can most likely be used for conversions in the future and this is it is probably best to just keep the latest.