Characterizing the reconstruction and enumerating the patterns of DNA sequences with re\-peats

DOI10.1007/S10878-007-9050-ZMaRDI QIDQ2471049zbMATH OpenOpenAlexFDO

Authors Hsun-Wen Chang, Pei-Fang (Jennifer) Tsai

Publication date 18 February 2008

Published in Journal of Combinatorial Optimization (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10878-007-9050-z

zbMATH Keywords

Catalan numberCombinatorial enumerationDNA digraphDNA sequencingPattern graphReduced digraph

Mathematics Subject Classification ID

Enumerative combinatorics (05A99) Applications of graph theory (05C90) Biochemistry, molecular biology (92C40)

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Cites work

• A course in combinatorics.
• Applied combinatorics.
• Approximate string-matching with q-grams and maximal matches
• Combinatorial algorithms for DNA sequence assembly
• Complexity of DNA sequencing by hybridization.
• DNA physical mapping and alternating Eulerian cycles in colored graphs
• DNA sequencing and string learning
• Euler circuits and DNA sequencing by hybridization
• scientific article; zbMATH DE number 1953078 (Why is no real title available?)
• scientific article; zbMATH DE number 1557065 (Why is no real title available?)
• On some properties of DNA graphs

Cited in

(5)

• Identification of repeats in DNA sequences using nucleotide distribution uniformity
• Using a VOM model for reconstructing potential coding regions in EST sequences
• Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences
• Self-matched Patterns, Golomb Rulers, and Sequence Reconstruction
• A Heuristic For Computing Repeats With A Factor Oracle: Application To Biological Sequences

Describes a project that uses

Uses Software

• RepeatAssembler

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