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

DOI10.1016/j.jtbi.2011.06.020zbMath1397.92459OpenAlexW2155430004WikidataQ35136642 ScholiaQ35136642MaRDI QIDQ1786038

Xue-Mei Liu, Fengzhu Sun, Jing Li, Michael S. Waterman, Lin Wan, Gesine D. 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) Protein sequences, DNA sequences (92D20) Genetics and epigenetics (92D10)

Related Items

Extraction of high quality \(k\)-words for alignment-free sequence comparison, Alignment free comparison: \(k\) word voting model and its applications, Large-Scale Multiple Sequence Alignment and Phylogeny Estimation

Uses Software

• EMBOSS
• CVTree3

Cites Work

• Empirical distribution of \(k\)-word matches in biological sequences
• Approximate word matches between two random sequences
• Characterizing the D2 Statistic: Word Matches in Biological Sequences
• A measure of the similarity of sets of sequences not requiring sequence alignment.
• A Measure of DNA Sequence Dissimilarity Based on Mahalanobis Distance between Frequencies of Words
• Asymptotic Behavior of k-Word Matches Between two Uniformly Distributed Sequences
• Distributional regimes for the number of k -word matches between two random sequences