Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition

DOI10.1111/J.0006-341X.2001.00441.XMaRDI QIDQ3078753zbMATH OpenOpenAlexWikidataFDO

Authors Tiee-Jian Wu, Ya-Ching Hsieh, Lung-An Li

Publication date 1 March 2011

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1111/j.0006-341x.2001.00441.x

zbMATH Keywords

dissimilarity measuresDNA sequencesKullback-Leibler discrepancyMahalanobis distanceMarkov chainstandardized Euclidean distance

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

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Cites work

• 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.
• Estimating the dimension of a model
• Hidden Markov chains and the analysis of genome structure
• scientific article; zbMATH DE number 194302 (Why is no real title available?)
• The Distribution of the Frequency of Occurrence of Nucleotide Subsequences, Based on Their Overlap Capability

Cited in

(26)

• A Poisson model of sequence comparison and its application to coronavirus phylogeny
• Use of image texture analysis to find DNA sequence similarities
• A novel statistical measure for sequence comparison on the basis of \(k\)-word counts
• New method for comparing DNA primary sequences based on a discrimination measure
• Alignment-free comparison of genome sequences by a new numerical characterization
• Weighted measures based on maximizing deviation for alignment-free sequence comparison
• Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition
• Numerical characteristics of word frequencies and their application to dissimilarity measure for sequence comparison
• Extraction of high quality \(k\)-words for alignment-free sequence comparison
• Statistical considerations underpinning an alignment-free sequence comparison method
• Study of LZ-word distribution and its application for sequence comparison
• Linear regression model of short k-word: a similarity distance suitable for biological sequences with various lengths
• Alignment free comparison: similarity distribution between the DNA primary sequences based on the shortest absent word
• Characterizing the D2 statistic: word matches in biological sequences
• Estimation of stratified mark-specific proportional hazards models with missing marks
• Prediction of high-risk types of human papillomaviruses using statistical model of protein ``sequence space
• A Measure of DNA Sequence Dissimilarity Based on Mahalanobis Distance between Frequencies of Words
• Genome Scanning Tests for Comparing Amino Acid Sequences Between Groups
• Distributional regimes for the number of k -word matches between two random sequences
• Investigating some attributes of periodicity in DNA sequences via semi-Markov modelling
• Overcoming the impossibility of age-balanced harvest
• Phylogenetic analysis of DNA sequences with a novel characteristic vector
• Vector representations and related matrices of DNA primary sequence based on \(L\)-tuple
• What's so special about Euclidean distance? A characterization with applications to mobility and spatial voting
• Spectral distortion measures for biological sequence comparisons and database searching
• Distribution of the number of matches between nucleotide sequences

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Uses Software

• FASTA

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