Variable length local decoding and alignment-free sequence comparison

DOI10.1016/J.TCS.2012.08.005MaRDI QIDQ690447zbMATH OpenOpenAlexWikidataFDO

Authors Gilles Didier, Eduardo Corel, Ivan Laprevotte, Claudine Landès-Devauchelle, Alexander Grossmann

Publication date 27 November 2012

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

Full work available at URL https://doi.org/10.1016/j.tcs.2012.08.005

zbMATH Keywords

algorithmprefix codecodinggenetic sequences comparison

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30) Algorithms on strings (68W32)

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Cites work

• A universal data compression system
• Coding with variable block maps
• The characterization of \(N\)-écritures and applications to the study of sequences of finally \(n+c^{st}\) complexity

Cited in

(7)

• scientific article; zbMATH DE number 2059987 (Why is no real title available?)
• Sequence graph transform (SGT): a feature embedding function for sequence data mining
• Four billion years: the story of an ancient protein family
• Introductory note on the draft paper ``Generalized affine signal analysis with time-delay thresholds, by Jan W. Dash, Alex Grossmann and Thierry Paul
• Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches
• Can we replace reads by numeric signatures? Lyndon fingerprints as representations of sequencing reads for machine learning
• Minimum message length encoding and the comparison of macromolecules

Describes a project that uses

Uses Software

• phyloXML
• DIALIGN-TX
• DIALIGN

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