Generalization of a suffix tree for RNA structural pattern matching

DOI10.1007/S00453-003-1067-9MaRDI QIDQ1879353zbMATH OpenOpenAlexFDO

Authors Tetsuo Shibuya

Publication date 22 September 2004

Published in Algorithmica (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s00453-003-1067-9

zbMATH Keywords

computational biology

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Data structures (68P05) Nonnumerical algorithms (68W05)

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• The structural border array
• Parameterized longest previous factor
• Secure parameterized pattern matching
• Variations of the parameterized longest previous factor
• Parameterized DAWGs: efficient constructions and bidirectional pattern searches
• Computing the parameterized Burrows-Wheeler transform online
• p-suffix sorting as arithmetic coding
• Compressed parameterized pattern matching
• Practical space-efficient index for structural pattern matching
• The affix array data structure and its applications to RNA secondary structure analysis
• scientific article; zbMATH DE number 1617275 (Why is no real title available?)
• On-line construction of parameterized suffix trees for large alphabets
• Pattern Discovery in RNA Secondary Structure Using Affix Trees
• Counting Parameterized Border Arrays for a Binary Alphabet
• Efficient pattern matching for RNA secondary structures
• A brief history of parameterized matching problems
• Verifying and enumerating parameterized border arrays
• The parameterized suffix tray
• Counter based suffix tree for DNA pattern repeats
• A prefix array for parameterized strings
• Direct linear time construction of parameterized suffix and LCP arrays for constant alphabets
• Large-scale frequent stem pattern mining in RNA families

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