Guide to the ApE (A Plasmid Editor) application
ApE is a piece of free software by Wayne Davis at the University of Utah. (We've already installed it in the labs, but you can download your own copy at home for macs, windows, and unix).
The easiest way to get your sequence(s) into ApE is to copy-and-paste. Be sure not to paste in the fasta label tags. You'll notice it warns you if you have illegal letters (ie, not ATGC) and will remove them.
To find Open Reading Frames (ORFs), you can use "Command+>" (That's the Command key plus "shift" plus "period". The command key is the one with an Apple on it by the space bar.) to move through the sequence selecting open reading frames. You can translate selected ORFs by pressing Command+T (or select "Translate" from the "ORFs" menu). If you use the One-letter code, the translation will be consistent with the translation provided by Pubmed.
To find particular sequences, press "Command+F" or click on the "microscope" icon or select "Find" under the "Edit" menu. Put the sequence you're looking for into the search field and click "Find next". You should be able to use this to find the transcription factor binding sites identified by JASPAR or from the BioinformaticsHandout.
To annotate a sequence, make sure it's highlighted and then select "New Feature" from the "Features" menu. Give the feature a name and use the pop-up menu at the bottom to identify the kind of feature, e.g. "Gene > cds" for the coding sequence or "Binding > protein_bind" for a transcription factor binding site).
To print your annotated DNA map, under the "Enzyme" menu select "Text Map", which will give a formatted page showing the entire sequence with your annotations. You'll notice that if you marked the coding sequence correctly, it will show you the translated amino acids. You can print this page out.
Finally, note that APE has many other useful and whizbang features not described by this guide. There's nothing stopping you from reading the manual or exploring the program further and discovering these features.