Vector seeds: An extension to spaced seeds

DOI10.1016/J.JCSS.2004.12.008MaRDI QIDQ1775772zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Broňa Brejová, Daniel G. Brown, Tomáš Vinař

Publication date 4 May 2005

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.2004.12.008

zbMATH Keywords

Sequence alignmentProbabilistic modelingHeuristic local alignmentHomology searchSpaced seeds

Mathematics Subject Classification ID

Problem solving in the context of artificial intelligence (heuristics, search strategies, etc.) (68T20) Protein sequences, DNA sequences (92D20)

Recommendations

• Rapid homology search with neighbor seeds
• Combinatorial Pattern Matching
• Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
• Spaced seeds for cross-species cDNA-to-genome sequence alignment
• New Algorithms for the Spaced Seeds

Cites work

• On spaced seeds for similarity search

Cited in

(8)

• Spaced seeds for cross-species cDNA-to-genome sequence alignment
• Combinatorial Pattern Matching
• Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
• Optimal spaced seeds for faster approximate string matching
• Computing and Combinatorics
• Rapid homology search with neighbor seeds
• Improved DNA-versus-protein homology search for protein fossils
• Subset Seed Automaton

Describes a project that uses

Uses Software

• BLAT

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