Mandala is a software to generate seed designs for seeded alignment algorithms. Mandala can be used to improve the sensitivity of alignment in practice.
Mandala can design near-optimal seeds for similarity models derived empirically from a collection of biosequences.
Mandala Sourc Code (C++)
:: MORE INFORMATION
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.