Java biosequence alignment applet

This applet demonstrates a prototype implementation of six algorithms for pairwise alignment described in the book Durbin et al: Biological Sequence Analysis, Cambridge University Press 1998, chapter 2. The applet requires Netscape 4.06 or later, or MS Internet Explorer 5 or later.

The applet

Type in two amino acid sequences (using the alphabet ARNDCQEGHILKMFPSTWYV) in the top-most two windows, then press the button.

E.g., try the example sequences HEAGAWGHEE and PAWHEAE from the book:

You must enable the execution of applets in your browser to see this applet

Links

A description of the implementation
The program source code
The additional applet user interface source code

Note that Microsoft Windows suffers from a limitation: a browser applet textfield can contain only approx. 50,000 characters; all excess characters are discarded. This is not a limitation of this program, of Java, or of Netscape.

Peter Sestoft (sestoft@itu.dk) 1999-09-27