title: New powerful statistics for alignment-free sequence comparison under a pattern transfer model.
abstract: Alignment-free sequence comparison is widely used for comparing gene regulatory regions and for identifying horizontally transferred genes. Recent studies on the power of a widely used alignment-free comparison statistic D2 and its variants D*2 and D(s)2 showed that their power approximates a limit smaller than 1 as the sequence length tends to infinity under a pattern transfer model. We develop new alignment-free statistics based on D2, D*2 and D(s)2 by comparing local sequence pairs and then summing over all the local sequence pairs of certain length. We show that the new statistics are much more powerful than the corresponding statistics and the power tends to 1 as the sequence length tends to infinity under the pattern transfer model.
authors: School of Physics, South China University of Technology, Guangzhou, PR China.
authors: Xuemei
authors: X
authors: Liu
authors: Lin
authors: L
authors: Wan
authors: Jing
authors: J
authors: Li
authors: Gesine
authors: G
authors: Reinert
authors: Michael S
authors: MS
authors: Waterman
authors: Fengzhu
authors: F
authors: Sun
mesh_terms: D000465:Algorithms; D000818:Animals; D003627:Data Interpretation, Statistical; D004330:Drosophila / Q000235:genetics; D019143:Evolution, Molecular; D015497:HIV-1 / Q000235:genetics; D015233:Models, Statistical; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid