BABA is an applet/java executable that aims to explain a few basic algorithms of bioinformatics.
You can get the source code on sourceforge
The applet covers:
- Basic Dynamic Programming table.
- Needleman & Wunsch algorithm, with score table.
- Smith & Waterman algorithm, with local alignment selection.
- Four Russians algorithm.
- Thanks to the great work of Patrick Dekker now B.A.B.A. includes the Nussinov algorithm! Cheers Patrick!
- May 2010: Fixed a few dumb indexing bugs on the interface. Thanks to all the kind people that have pointed them out.
- April 2014: Fixed bad starting gap values in Smith-Waterman. A big thank you to Ishwar.
- April 2014: Added a standalone runnable version
- October 2014: Fixed flipped indexes in the interface
- March 2015: Refactored/cleaned up the code, added "history" to show all the arrows computed in the process.
Since java applets have become a sort of security liability in the last few years, you
might have troubles running the applet. If you have java installed, you can
download the runnable version and just double
click it to run it.
- In unix the scolling panel does not behave properly.
- Cut&Paste sometimes doesn't work within the strings set.
Note: A loooooong while ago I wrote a report and
a powerpoint presentation on BABA. It's outdated now but
it might be a good starting point if you want to modify the source.
For any question e-mail me at norman.casagrande (at) yahoo (dot) com