Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Improved alignment of nucleosome DNA sequences using a mixture model.

Ji-Ping Z Wang1, Jonathan Widom

  • 1Department of Statistics, 2006 Sheridan Road, Evanston, IL 60208, USA. jzwang@northwestern.edu

Nucleic Acids Research
|December 13, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

PloS one·2015
Same author

In vitro selection of DNAs with an increased propensity to form small circles.

Biopolymers·2015
Same author

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.

Proceedings of the National Academy of Sciences of the United States of America·2014
Same author

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.

eLife·2014
Same author

High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster.

Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research·2014
Same author

A locally convoluted cluster model for nucleosome positioning signals in chemical map.

Journal of the American Statistical Association·2014

This study introduces a new probabilistic model to align nucleosomal DNA sequences, revealing inherent periodic patterns. The improved alignment enhances sequence identity and periodicity, overcoming limitations of traditional methods.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Nucleosomal DNA exhibits weak sequence similarity, challenging traditional alignment methods.
  • A known ~10 bp periodicity of dinucleotide signals exists in nucleosomal DNA.
  • Existing alignment tools struggle to capture these subtle sequence periodicities.

Purpose of the Study:

  • To develop a probabilistic mixture model for improved alignment of nucleosomal DNA sequences.
  • To characterize and leverage the ~10 bp dinucleotide periodicity for better sequence alignment.
  • To enhance the identification of sequence patterns within nucleosomal DNA.

Main Methods:

  • Developed a probabilistic mixture model incorporating dinucleotide periodicity.
  • Modeled statistically significant dinucleotide signals (AA/TT, GC, TA) with phase shifts.

Related Experiment Videos

  • Aligned DNA sequences by maximizing likelihood for both Watson and Crick strands.
  • Utilized Fourier analysis to assess alignment quality.

    • Main Results:

    • The new model successfully aligned 177 chicken nucleosomal DNA sequences.
    • All 10 dinucleotides were found to be periodic, with two distinct phases and varying intensities.
    • The developed alignment demonstrated enhanced periodicity and sequence identity compared to center alignment.
    • Fourier analysis confirmed improved periodicity in the new alignment.

    Conclusions:

    • The probabilistic mixture model significantly improves nucleosomal DNA sequence alignment.
    • The findings reveal a more comprehensive understanding of sequence periodicities within nucleosomes.
    • This approach offers a powerful tool for analyzing DNA sequences in the context of chromatin structure.