ArticleNucleic acids research2005
Improved alignment of nucleosome DNA sequences using a mixture model.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.Nucleic acids research · 2025Article
- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- Methylation Status ofCell journal · 2021Article
- Distinctive regulatory architectures of germline-active and somatic genes inGenome research · 2020Article
- VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.Nucleic acids research · 2019Article
- Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping.Trends in genetics : TIG · 2017Review
- A locally convoluted cluster model for nucleosome positioning signals in chemical map.Journal of the American Statistical Association · 2014Article
- High-resolution nucleosome mapping of targeted regions using BAC-based enrichment.Nucleic acids research · 2013Article
- Article
- A generalized hidden Markov model for determining sequence-based predictors of nucleosome positioning.Statistical applications in genetics and molecular biology · 2012Article
- Nucleosome positioning in Saccharomyces cerevisiae.Microbiology and molecular biology reviews : MMBR · 2011Review
- Article
- Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.PLoS computational biology · 2010Article
- Predicting nucleosome positioning using a duration Hidden Markov Model.BMC bioinformatics · 2010Article
- The DNA sequence-dependence of nucleosome positioning in vivo and in vitro.Journal of biomolecular structure & dynamics · 2010Article
- Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches.Epigenetics · 2010Article
- Intrinsic flexibility of B-DNA: the experimental TRX scale.Nucleic acids research · 2010Article
- Nucleosome positioning and gene regulation: advances through genomics.Nature reviews. Genetics · 2009Review
- Preparation and analysis of uniquely positioned mononucleosomes.Methods in molecular biology (Clifton, N.J.) · 2009Article
- Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.PLoS computational biology · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA sequences that are present in nucleosomes have a preferential approximately 10 bp periodicity of certain dinucleotide signals, but the overall sequence similarity of the nucleosomal DNA is weak, and traditional multiple sequence alignment tools fail to yield meaningful alignments. We develop a mixture model that characterizes the known dinucleotide periodicity probabilistically to improve the alignment of nucleosomal DNAs. We assume that a periodic dinucleotide signal of any type emits according to a probability distribution around a series of 'hot spots' that are equally spaced along nucleosomal DNA with 10 bp period, but with a 1 bp phase shift across the middle of the nucleosome. We model the three statistically most significant dinucleotide signals, AA/TT, GC and TA, simultaneously, while allowing phase shifts between the signals. The alignment is obtained by maximizing the likelihood of both Watson and Crick strands simultaneously. The resulting alignment of 177 chicken nucleosomal DNA sequences revealed that all 10 distinct dinucleotides are periodic, however, with only two distinct phases and varying intensity. By Fourier analysis, we show that our new alignment has enhanced periodicity and sequence identity compared with center alignment. The significance of the nucleosomal DNA sequence alignment is evaluated by comparing it with that obtained using the same model on non-nucleosomal sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.