Alignment-free comparison of genome sequences by a new numerical characterization

DOI10.1016/J.JTBI.2011.04.003MaRDI QIDQ1783550zbMATH OpenOpenAlexWikidataFDO

Authors Guohua Huang, Houqing Zhou, Yong-Fan Li, Lixin Xu

Publication date 21 September 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2011.04.003

zbMATH Keywords

phylogenetic treeDNA sequencegraphical representationalignment-free comparisonnumerical characterization

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

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Cites work

• A 3D graphical representation of DNA sequences and its application
• A Measure of DNA Sequence Dissimilarity Based on Mahalanobis Distance between Frequencies of Words
• A measure of the similarity of sets of sequences not requiring sequence alignment.
• Distributional regimes for the number of k -word matches between two random sequences
• New 3D graphical representation of DNA sequence based on dual nucleotides
• Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition

Cited in

(17)

• Compositional spectrum - revealing patterns for genomic sequence characterization and comparison
• Efficient Alignment Free Sequence Comparison with Bounded Mismatches
• Alignment-free sequence comparison with spaced k-mers.
• A novel representation of DNA sequence based on CMI coding
• Sequence comparison via polar coordinates representation and curve tree
• Theoretical Computer Science
• Alignment-free sequence comparison for biologically realistic sequences of moderate length
• A new combinatorial approach to sequence comparison
• Comparison of numerical representations of genomic sequences: choosing the best mapping for wavelet analysis
• GAME: A simple and efficient whole genome alignment method using maximal exact match filtering
• Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization
• Comparison of Symbol Sequences: No Editing, No Alignment
• New method for global alignment of 2 DNA sequences by the tree data structure
• Discrete wavelet packet transform based discriminant analysis for whole genome sequences
• New powerful statistics for alignment-free sequence comparison under a pattern transfer model
• Circular helix-like curve: an effective tool of biological sequence analysis and comparison
• Biomolecular topology: modelling and analysis

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