Sensitivity analysis and efficient method for identifying optimal spaced seeds

DOI10.1016/J.JCSS.2003.04.002MaRDI QIDQ1878677zbMATH OpenOpenAlexFDO

Authors Louxin Zhang, Kwok Pui Choi

Publication date 8 September 2004

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.2003.04.002

Mathematics Subject Classification ID

Pattern recognition, speech recognition (68T10)

Recommendations

• New Algorithms for the Spaced Seeds
• Combinatorial Pattern Matching
• On spaced seeds for similarity search
• On the complexity of the spaced seeds
• Optimal spaced seeds for hidden Markov models, with application to homologous coding regions

Cites work

• A Combinatorial Identity and Its Application to the Problem Concerning the First Occurrence of a Rare Event
• A measure of the similarity of sets of sequences not requiring sequence alignment.
• A time-efficient, linar-space local similarity algorithm
• Distribution Theory of Runs: A Markov Chain Approach
• Efficient randomized pattern-matching algorithms
• scientific article; zbMATH DE number 1786448 (Why is no real title available?)
• Multiple filtration and approximate pattern matching
• On spaced seeds for similarity search
• Run Probabilities in Sequences of Markov-Dependent Trials
• Runs and scans with applications

Cited in

(10)

• Analytic combinatorics for computing seeding probabilities
• On the complexity of the spaced seeds
• The Minimum Barrier Distance – Stability to Seed Point Position
• Sequential Methods for Monitoring Declining Quality, with Application to the Long-Term Storage of Seeds
• Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
• New Algorithms for the Spaced Seeds
• Combinatorial Pattern Matching
• BDD-BASED ANALYSIS OF GAPPED q-GRAM FILTERS
• Hardness of optimal spaced seed design
• Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design

Describes a project that uses

Uses Software

• PatternHunter

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