Alignment Using BioEdit

BioEdit is, among other things, an alignment editor, although it has many more capabilities. It is available free from the Department of Molecular Biology at North Carolina State University.

Start BioEdit. From the File menu, select Open.

When your chimp and human sequences are loaded, the BioEdit window should look like this:

Now go to the Sequence menu:

Choose Pairwise Alignment.

The result will look like this:

You can save the contents of the small text window, if desired. I usually don't.

Go to the File menu again and select Graphic View:

A new window will appeaar:

Use the check boxes at the top of the window to control how the result is displayed.

When the display suits you, go to the Edit menu:

The options place the graphic view on the clipboard, from where you can paste it into a document.

BioEdit will only align two sequences. If you have more than two go to the Accessory Applications menu and choose clustalW:

Once the alignment is done, you can manipulate it in Graphic View as above.

BioEdit will also translate DNA or RNA to protein, find cDNA or the reverse complement, do a nice analysis with bar graph of the percentages of the four bases, and otherwise characterize your sequence.

For example, with your human insulin gene loaded and selected, choose Sequence/Nucleic Acid/Translate/Frame 1. You will get a new window containing the translation. Try this when you have a sequence displayed in Graphic View also.


This page last modified 3:08 PM on Monday February 8th, 2010.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469