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BABA
Basic-Algorithms-of-Bioinformatics
Applet
Why?
Interactive demos helps a lot to
understand a problem
 Very few interactive works available on the
net

only for simple dynamic programming
 limited parameters
 really ugly
 source code rarely available

Goals

Make algorithms fully understandable and
interactive:
Simple Dynamic Programming Table
 Needleman & Wunsch
 Smith & Waterman Local Search
 Four Russians

Easy to use
 Highlight the important aspects
 Let the user play with the parameters

Implementation

Java 1.2 compatible

Applet running on


Browser (on the net)

Applet viewer
Swing + Graphics 2D: nice to see!
Basic layout for other DP
algorithms

Easy to extend!


The four algorithms extends
 The
basic graphic grid class
 The
interface
 The
algorithm execution model
published under GPL
Let’s see some action!
Info
~ 8600 lines of code
 Basic Grid


DP Grid
 NW

 FR

Grid
SW Grid
Grid
Basic DP Algorithm

NW Algorithm
 SW Algorithm

Four Russians