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Good spaced seeds for homology search
Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering
Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma, Tromp and Li (2002) discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. Results: Our numerical computation shows that the ranks of spaced seeds (based ondoi:10.1109/bibe.2004.1317368 dblp:conf/bibe/ChoiZZ04 fatcat:achdiwprbngddjwdleueq74odq