Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections

DOI10.1007/978-3-540-89097-3_17MaRDI QIDQ5505395zbMATH OpenOpenAlexFDO

Authors Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro

Publication date 27 January 2009

Published in String Processing and Information Retrieval (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-540-89097-3_17

Mathematics Subject Classification ID

Data structures (68P05) Information storage and retrieval of data (68P20) Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30)

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Cited in

(26)

• FM-index of alignment with gaps
• A faster implementation of online RLBWT and its application to LZ77 parsing
• Flexible indexing of repetitive collections
• Top tree compression of tries
• Sparse binary relation representations for genome graph annotation
• Wavelet trees for all
• Fast relative Lempel-Ziv self-index for similar sequences
• An improved algorithm for the all-pairs suffix-prefix problem
• Sensitivity of string compressors and repetitiveness measures
• Indexing highly repetitive collections
• Composite repetition-aware data structures
• Efficient construction of a compressed de Bruijn graph for pan-genome analysis
• FM-index of alignment: a compressed index for similar strings
• Self-indexing based on LZ77
• Self-indexed Text Compression Using Straight-Line Programs
• Algorithms for indexing highly similar DNA sequences
• Storage and Retrieval of Individual Genomes
• On compressing and indexing repetitive sequences
• scientific article; zbMATH DE number 7559178 (Why is no real title available?)
• Linking BWT and XBW via Aho-Corasick automaton: applications to run-length encoding
• LZ-End Parsing in Linear Time
• Byte-aligned pattern matching in encoded genomic sequences
• Fast label extraction in the CDAWG
• Lazy Lempel-Ziv factorization algorithms
• String Indexing with Compressed Patterns
• LZ77 computation based on the run-length encoded BWT

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