New Algorithms for the Spaced Seeds

DOI10.1007/978-3-540-73814-5_5MaRDI QIDQ3612577zbMATH OpenOpenAlexFDO

Authors Xin Gao, Shuai Cheng Li, Yinan Lu

Publication date 10 March 2009

Published in Frontiers in Algorithmics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-540-73814-5_5

zbMATH Keywords

bioinformaticshomology searchspaced seed

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Algorithms on strings (68W32) Computational methods for problems pertaining to biology (92-08)

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(10)

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• An index structure for spaced seed search
• Better spaced seeds using quadratic residues
• Languages of lossless seeds
• Fast spaced seed hashing
• Combinatorial Pattern Matching
• Spaced seeds for cross-species cDNA-to-genome sequence alignment

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