New powerful statistics for alignment-free sequence comparison under a pattern transfer model

DOI10.1016/J.JTBI.2011.06.020zbMATH Open1397.92459OpenAlexW2155430004WikidataQ35136642 ScholiaQ35136642MaRDI QIDQ1786038FDOQ1786038

Authors Xuemei Liu, Lin Wan, Jing Li, Michael S. Waterman, Fengzhu Sun, Gesine Reinert 

Publication date 24 September 2018

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

Full work available at URL http://europepmc.org/articles/pmc3146591

zbMATH Keywords

alignment-free sequence comparison\(D_2\)pattern transfer model

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20)

Recommendations

• Statistical considerations underpinning an alignment-free sequence comparison method
• Alignment-free comparison of genome sequences by a new numerical characterization
• Alignment-free sequence comparison for biologically realistic sequences of moderate length
• Alignment-free sequence comparison with spaced k-mers.
• Efficient Alignment Free Sequence Comparison with Bounded Mismatches
• Weighted measures based on maximizing deviation for alignment-free sequence comparison
• A systematic comparison of various statistical alignment models
• Alignment Statistics for Long-Range Correlated Genomic Sequences

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.
• Approximate word matches between two random sequences
• Asymptotic Behavior of k-Word Matches Between two Uniformly Distributed Sequences
• Characterizing the D2 statistic: word matches in biological sequences
• Distributional regimes for the number of k -word matches between two random sequences
• Empirical distribution of \(k\)-word matches in biological sequences

Cited In (7)

• Alignment-free sequence comparison with spaced k-mers.
• Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
• Extraction of high quality \(k\)-words for alignment-free sequence comparison
• Alignment-free sequence comparison for biologically realistic sequences of moderate length
• Alignment free comparison: \(k\) word voting model and its applications
• On an alternative sequence comparison statistic of Steele
• Statistical considerations underpinning an alignment-free sequence comparison method

Uses Software

• EMBOSS
• CVTree3

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