Linear regression model of short k-word: a similarity distance suitable for biological sequences with various lengths.
Originating from sequences' length difference, both k-word based methods and graphical representation approaches have uncovered biological information in their distinct ways. However, it is less likely that the mechanisms of information storage vary with sequences' length. A similarity distance suitable for sequences with various lengths will be much near to the mechanisms of information storage. In this paper, new sub-sequences of k-word were extracted from biological sequences under a one-to-one mapping. The new sub-sequences were evaluated by a linear regression model. Moreover, a new distance was defined on the invariants from the linear regression model. With comparison to other alignment-free distances, the results of four experiments demonstrated that our similarity distance was more efficient.
School of Mathematical Sciences, Dalian University of Technology, Dalian, Liaoning 116024, PR China; School of Mathematics, Liaoning Normal University, Dalian, Liaoning 116029, PR China. Electronic address: cinema@lnnu.edu.cn.
Xiwu
X
Yang
School of Mathematical Sciences, Dalian University of Technology, Dalian, Liaoning 116024, PR China.
Tianming
T
Wang
D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D005091:Exons / Q000235:genetics; D006801:Humans; D016018:Least-Squares Analysis; D016014:Linear Models; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D055544:beta-Globins / Q000235:genetics
D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S; D055544:beta-Globins
Alignment-free; Bootstrap; Phylogenetic tree; Sequence comparison