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Joint with Department of Computer Science Monday, March 3, 2003 10:30 AM in REC 227 Dr. Uri Keich University of California, San Diego will speak on On Designing Seeds for Similarity Search in Genomic DNA Abstract Large-scale similarity searches of genomic DNA are of fundamental importance in annotating functional elements in genomes. To perform large comparisons efficiently, BLAST and other widely used tools use seeded alignment, which compares only sequences that can be shown to share a common pattern or "seed" of matching bases. The choice of seed substantially affects the sensitivity of seeded alignment, but designing and evaluating optimal seeds is computationally challenging. In this talk I will address some of the computational problems arising in seed design.
The talk will rely on joint works with Ming Li, Bin Ma and John Tromp,
Jeremy Buhler and Yanni Sun.
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