Dina workshop: Java biosequence alignment applet
This applet demonstrates algorithms for pairwise alignment described
in the book Durbin et al: Biological Sequence Analysis, Cambridge
University Press 1998, chapter 2.
Another page demonstrates construction and
drawing of phylogenetic trees.
The alignment program
Type in two amino acid sequences (using the alphabet
ARNDCQEGHILKMFPSTWYV) in the top-most two windows, then press the
E.g., try the example sequences HEAGAWGHEE and PAWHEAE:
- This version includes Global, Local, Affine Global, Smart
Global, and Smart Affine Local alignment.
- The linear gap cost algorithms charge 8*k for a gap of length k.
- The affine gap cost algorithms charge 10+2*k for a gap of length
- You may use letters from the alphabet
- All other characters are ignored, including spaces etc.
- To copy sequences from other web pages, mark them using the mouse,
press Ctrl+C, point at a textfield in the applet, and press Ctrl+V.
- The value -Inf means minus infinity.
- To print the contents of the textarea, select the text, copy it
to a text editor (e.g. WordPad) and print it from there, preferably
using a fixed-width font such as Courier.
Note that Microsoft Windows suffers from a limitation: a browser
applet text component 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 (email@example.com) 2000-04-05