Indexing factors with gaps

DOI10.1007/S00453-007-9141-3MaRDI QIDQ2391183zbMATHOpenAlexFDO

Authors Costas S. Iliopoulos, M. Sohel Rahman

Publication date 24 July 2009

Published in Algorithmica (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s00453-007-9141-3

zbMATH Keywords

algorithmsdata structuresuffix treegapped-factorstring index

Mathematics Subject Classification ID

Data structures (68P05) Algorithms on strings (68W32)

Recommendations

• Indexing Factors with Gaps
• INDEXING GAPPED-FACTORS USING A TREE
• Index of lacunarity
• Gapped indexing for consecutive occurrences
• Gapped indexing for consecutive occurrences
• FM-index of alignment with gaps
• Index for factors generated by extended Jones' projections
• Factor-based robust index tracking
• Choosing a dynamic common factor as a coincident index

Cites work

• scientific article; zbMATH DE number 1615292 (Why is no real title available?)
• scientific article; zbMATH DE number 3913711 (Why is no real title available?)
• scientific article; zbMATH DE number 1947378 (Why is no real title available?)
• scientific article; zbMATH DE number 2038766 (Why is no real title available?)
• scientific article; zbMATH DE number 2119724 (Why is no real title available?)
• A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS
• A Space-Economical Suffix Tree Construction Algorithm
• Algorithms on Strings, Trees and Sequences
• Combinatorial Pattern Matching
• Constructing suffix arrays in linear time
• Dictionary matching and indexing with errors and don't cares
• Finding Patterns with Variable Length Gaps or Don’t Cares
• Jewels of Stringology
• Longest repeats with a block of \(k\) don't cares
• On-line construction of suffix trees
• Space efficient linear time construction of suffix arrays
• Suffix Arrays: A New Method for On-Line String Searches
• Text indexing with errors

Cited in

(14)

• Longest common prefix with mismatches
• String indexing for top-\(k\) close consecutive occurrences
• Substring Range Reporting
• Document retrieval with one wildcard
• INDEXING GAPPED-FACTORS USING A TREE
• Indexing a sequence for mapping reads with a single mismatch
• Gapped indexing for consecutive occurrences
• Orthogonal range searching for text indexing
• Substring range reporting
• Gapped indexing for consecutive occurrences
• Indexing Factors with Gaps
• Reporting consecutive substring occurrences under bounded gap constraints
• Reporting consecutive substring occurrences under bounded gap constraints
• Less space: indexing for queries with wildcards

Describes a project that uses

Uses Software

• LAGAN
• MUSCLE
• PatternHunter

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