Better spaced seeds using quadratic residues

DOI10.1016/J.JCSS.2013.03.002MaRDI QIDQ394336zbMATH OpenOpenAlexFDO

Authors Lavinia Egidi, Giovanni Manzini

Publication date 27 January 2014

Published in Journal of Computer and System Sciences (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcss.2013.03.002

zbMATH Keywords

Hamming distanceapproximate matchinghomology searchlossless filtrationsequence comparisonspaced seeds

Mathematics Subject Classification ID

Power residues, reciprocity (11A15) Algorithms on strings (68W32)

Recommendations

• Design and analysis of periodic multiple seeds
• Spaced seed design using perfect rulers
• On spaced seeds for similarity search
• New Algorithms for the Spaced Seeds
• Optimal spaced seeds for faster approximate string matching

Cites work

• scientific article; zbMATH DE number 1998337 (Why is no real title available?)
• scientific article; zbMATH DE number 1786448 (Why is no real title available?)
• Combinatorial Designs
• Hardness of optimal spaced seed design
• On spaced seeds for similarity search
• On the Distribution of Quadratic Residues and Nonresidues Modulo a Prime Number
• On the complexity of the spaced seeds
• Optimal spaced seeds for faster approximate string matching
• Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
• Spaced seed design using perfect rulers

Cited in

(7)

• New Algorithms for the Spaced Seeds
• Design and analysis of periodic multiple seeds
• Languages of lossless seeds
• Spaced seed design using perfect rulers
• Secure function extensions to additively homomorphic cryptosystems
• Fast spaced seed hashing
• Compressed spaced suffix arrays

Describes a project that uses

Uses Software

• ZOOM
• YASS
• PatternHunter
• BLAST
• PSI-BLAST
• SHRiMP
• BLAT

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