Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach

By Ji Qi, Bin Wang, Bainian Hao. Journal of Molecular Evolution, 2003

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Prediction of protein structural classes for low-homology sequences based on predicted secondary structure (2010, neutral): “The recurrence quantification analysis aims to capture the sequence order information of the time series [17], the K-string based information entropy to reflect certain local interactions along the secondary structure [18], and the segment-based analysis to characterize the spacial arrangements of a”
Alignment-free sequence comparison: benefits, applications, and tools (2017, background): “…using various sets of simulated DNA sequences [54, 135, 136], primate/mammalian mitochondrial genomes [40, 61, 137, 138], whole prokaryotic genomes/proteomes [117, 139], selected plant genomes [121, 140], small subsets of homologous genes [141, 142], and different combinations thereof [36, 139].”