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Designing Multiple Simultaneous Seeds for DNA Similarity Search
2005
Journal of Computational Biology
The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of sequences sharing a common short "seed," or pattern of matching residues. Some of these changes raise the possibility of improving search performance by probing sequence pairs with several distinct seeds, any one of which is sufficient for a seed match. However, designing a set of seeds to maximize their combined
doi:10.1089/cmb.2005.12.847
pmid:16108721
fatcat:ym6sy3we6fcovpsfyp5g7hih5m