Using APE

If APE is not currently installed on this computer, search APE plasmid on google, and download the software for the appropriate system.

APE can open the .seq and .ab1 files in which sequencing results are typically formatted.

Blasting Two Sequences

Open two sequences on APE, then select Tools, Align Two Sequences. The alignment read use red highlighting wherever bases don't properly match up. Double-clicking on any base pair will bring up the sequence page for that strand with the cursor at the location that corresponds to the clicked base. On the sequence page, going to Feature, New Feature allows the highlighting and annotating of certain regions, making it much easier to remember where important sequences are and why they are important. Remember that APE can also save these annotated files, so that the modified versions can be easily referenced in the future.

Cloning DNA

APE can help plan and check cloning, restriction digests and related experiments. Open a sequence in APE and go to Enzymes. Here, various tools that can help in digests are available, such as Enzyme List, which shows a list of REs and the number of sites in the sequence for each one. By clicking select, the sites for the selected RE will be highlighted. Graphic map presents another way of viewing similar data. Digestion will show the expected lengths of bands that should appear if the results of a digestion of this sequence with the selected REs were to be run on a gel.

Under ORFs, find next and find previous find sequences that begin in an ATG and end in a stop sequence. By selecting Selection Translate, the amino acid sequence for the current selection will be displayed.

-- Main.AurkoDasgupta - 08 Jul 2011