This is the home page of the Mandala software to generate seed designs for seeded alignment algorithms. It was first presented at RECOMB 2003 in the following paper (PDF available online):
J. Buhler, U. Keich, and Y. Sun. "Designing Seeds for Similarity Search in Genomic DNA." In Proceedings of the Seventh Annual Internation Conference on Computational Molecular Biology, Berlin, Germany, 67-75, 2003.
Version 1.1 adds a greatly improved method for multi-seed design. These extensions were described in the following paper at RECOMB 2004:
Y. Sun and J. Buhler. "Designing Multiple Simultaneous Seeds for DNA Similarity Search." In Proceedings of the Eighth Annual Internation Conference on Computational Molecular Biology, San Diego, California, 2004.
Continuing research and development of Mandala is funded as part of National Science Foundation Grant DBI-0237903. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Mandala version 1.1.1 is now available. Further development to incorporate new models and optimization procedures is ongoing.
Version 1.1.1 is a minor update to v1.1 to fix a compilation issue exposed by g++ 3.4.0.