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:
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.
# Baba config example # Valid gap costs: # (a) a value: 4 or -1 (will be repeated over the string) # (b) a sequence: 1,3,5 or {1, 4, 2} (must have the same length of the string) # (c) an empty string: interpreted as sequence starting from 1. # Valid score tables: PAM250, BLOSUM50, BLOSUM62, VTML160, PENALIZEMISMATCH_1, PENALIZEMISMATCH_2, PENALIZEMISMATCH_3 [simple_dp] S1=END s2=SEND s1_gap_cost= s2_gap_cost=-4 [needleman_wunsch] s1=HEAGAWGHEE s2=PAWHEAE score_table=BLOSUM62 s1_gap_cost=-6 s2_gap_cost=-6 [smith_waterman] s1=HEAGAWGHEE s2=PAWHEAE score_table= s1_gap_cost= s2_gap_cost= [four_russians] s1=ATGTCA s2=ATTAGTCA [nussinov] s1=GGGAAAUCC score_table=
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 It's outdated now but it might be a good starting point if you want to modify the source.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