ArticleJournal of theoretical biology2011
New powerful statistics for alignment-free sequence comparison under a pattern transfer model.
Article in Journal of theoretical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.Scientific reports · 2021Article
- The statistical power ofSynthetic and systems biotechnology · 2019Article
- A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.Briefings in bioinformatics · 2019Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
- Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.Bioinformatics (Oxford, England) · 2016Article
- On the comparison of regulatory sequences with multiple resolution Entropic Profiles.BMC bioinformatics · 2016Article
- Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences.BioMed research international · 2015Article
- Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.Briefings in bioinformatics · 2014Review
- Alignment-free protein interaction network comparison.Bioinformatics (Oxford, England) · 2014Article
- New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.Briefings in bioinformatics · 2014Review
- Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.BMC bioinformatics · 2014Article
- Multiple alignment-free sequence comparison.Bioinformatics (Oxford, England) · 2013Article
- A geometric interpretation for local alignment-free sequence comparison.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Alignment-free sequence comparison based on next-generation sequencing reads.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.PloS one · 2013Article
- Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.Bioinformatics (Oxford, England) · 2012Article
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6 authors.
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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.
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