FM-index of alignment: a compressed index for similar strings

DOI10.1016/j.tcs.2015.08.008zbMath1345.68123OpenAlexW1201605537MaRDI QIDQ294964

Heejin Park, Martine Léonard, Joong Chae Na, Thierry Lecroq, Laurent Mouchard, Kun Soo Park, Hyun-Joon Kim

Publication date: 16 June 2016

Published in: Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.tcs.2015.08.008

zbMATH Keywords

alignmentsbackward searchFM-indexesindexes for similar stringssuffix arrays

Mathematics Subject Classification ID

Database theory (68P15) Genetics and epigenetics (92D10) Data structures (68P05) Information storage and retrieval of data (68P20)

Related Items (7)

Wheeler graphs: a framework for BWT-based data structures ⋮ Algorithms and complexity on indexing founder graphs ⋮ FM-index of alignment with gaps ⋮ Pattern Matching on Elastic-Degenerate Text with Errors ⋮ Lightweight merging of compressed indices based on BWT variants ⋮ Haplotype-aware graph indexes ⋮ Unnamed Item

Cites Work

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• Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval
• Indexing compressed text
• Indexing Similar DNA Sequences
• Storage and Retrieval of Individual Genomes
• A universal algorithm for sequential data compression
• Algorithms on Strings, Trees and Sequences
• Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections

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