We have built a Java GUI on top of BioJava for cis-regulatory sequence analysis, especially in higher eukaryotes. It is linked with Ensembl for the retrieval of genes and intergenic sequences and with several algorithms for comparative genomics and motif detection (using SOAP web services).
The description of the program, the jar file, Java Web Start version, tutorial, manual, etc. can be found here: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.
Currently the classes cannot be used directly from the API, and I have no good Javadocs at present. If people would find it useful, I could consider cleaning up my code for this purpose.
Thank you BioJava!
Best regards & all comments are appreciated,
Stein Aerts.
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Stein Aerts BioI@SISTA
K.U.Leuven ESAT-SCD Belgium
http://www.esat.kuleuven.ac.be/~dna/BioI
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