Basic-Algorithms-of-Bioinformatics Applet

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:

Sorry, your browser does not support Java. Please go to http://www.oracle.com/technetwork/java/javase/downloads/index.html to download it.


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.

Screenshots

Useful Links

Known bugs

Example Configuration File

# 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 It's outdated now but it might be a good starting point if you want to modify the source.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