Byte-aligned pattern matching in encoded genomic sequences

DOI10.4230/LIPICS.WABI.2017.20MaRDI QIDQ5111826zbMATH OpenFDO

Authors Jan Holub, P. P. Procházka

Publication date 27 May 2020

Full work available at URL https://doi.org/10.4230/LIPICS.WABI.2017.20

zbMATH Keywords

\(q\)-gram inverted indexgenomic sequencespattern matching

Mathematics Subject Classification ID

Software, source code, etc. for problems pertaining to biology (92-04) Protein sequences, DNA sequences (92D20)

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Cites work

• A fast string searching algorithm
• A fast suffix automata based algorithm for exact online string matching
• An algorithm for approximate membership checking with application to password security
• Compressed suffix arrays and suffix trees with applications to text indexing and string matching (extended abstract)
• Fast and flexible packed string matching
• Fast Pattern Matching in Strings
• scientific article; zbMATH DE number 2185629 (Why is no real title available?)
• scientific article; zbMATH DE number 432779 (Why is no real title available?)
• scientific article; zbMATH DE number 140453 (Why is no real title available?)
• scientific article; zbMATH DE number 801745 (Why is no real title available?)
• Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections
• Tuning BNDM with \(q\)-grams

Cited in

(2)

• BAPM
• Sequence matching with binary codes

Describes a project that uses

Uses Software

• GLIMPSE

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