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

Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations.

Jure Zupan1, Milan Randić

  • 1National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia 61115. jure.zupan@ki.si

Journal of Chemical Information and Modeling
|April 6, 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

Erratum: Self-Consistent Extraction of Spectroscopic Bounds on Light New Physics [Phys. Rev. Lett. 130, 121801 (2023)].

Physical review letters·2025
Same author

Self-Consistent Extraction of Spectroscopic Bounds on Light New Physics.

Physical review letters·2023
Same author

New physics searches at kaon and hyperon factories.

Reports on progress in physics. Physical Society (Great Britain)·2022
Same author

Erratum to: Anomaly free Froggatt-Nielsen models of flavor.

Journal of high energy physics : JHEP·2022
Same author

Synergistic and antagonistic effects of immunomodulatory drugs on the action of antifungals against <i>Candida glabrata</i> and <i>Saccharomyces cerevisiae</i>.

PeerJ·2018
Same author

Quorum-sensing in yeast and its potential in wine making.

Applied microbiology and biotechnology·2016
Same journal

Correction to "AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus".

Journal of chemical information and modeling·2026
Same journal

MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.

Journal of chemical information and modeling·2026
Same journal

Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.

Journal of chemical information and modeling·2026
Same journal

Structural and Thermodynamic Discrimination between Agonists and Antagonists of Retinoic Acid Receptor γ and the Vitamin D Receptor.

Journal of chemical information and modeling·2026
Same journal

PACEff Builder: An Efficient Platform for Constructing PACE Hybrid-Resolution Models for Molecular Dynamics Simulations of Aqueous Protein, Peptide Assembly, and Membrane Protein Systems.

Journal of chemical information and modeling·2026
Same journal

TransKla: A Local-Global Cross-Attention Based Transformer Approach for Prediction of Lysine Lactylation Sites.

Journal of chemical information and modeling·2026
See all related articles

A novel algorithm encodes biological sequences like DNA and amino acids into visual representations. This method allows for flexible dimensionality and aids in comparing genetic data across species.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biological sequences, such as DNA and amino acids, are fundamental to life.
  • Efficient methods for analyzing and visualizing these complex sequences are crucial for biological research.
  • Existing encoding methods may lack flexibility or intuitive visualization capabilities.

Purpose of the Study:

  • To propose a new algorithm for encoding long biological strings into "zigzag" or "spectrum-like" representations.
  • To offer a flexible encoding scheme adaptable to different dimensionalities (3D, 2D, or 1D).
  • To demonstrate the utility of this encoding scheme for comparative analysis of biological sequences.

Main Methods:

  • Development of a novel encoding algorithm for biological sequences.

Related Experiment Videos

  • Implementation of the algorithm to generate "zigzag" or "spectrum-like" representations.
  • Variable dimensionality (3D, 2D, 1D) encoding based on user preference.
  • Utilizing initial positioning of sequence units for encoding.
  • Application to visualize and compare beta globin gene exon strings from multiple species.

    • Main Results:

    • Successful encoding of DNA bases, amino acids, and base triplets into multi-dimensional representations.
    • Demonstration of the algorithm's ability to generate "zigzag" and "spectrum-like" visual outputs.
    • Visual and chemometric comparison of beta globin gene sequences from 10 different species was achieved.
    • The encoding scheme proved effective for comparative analysis of genetic data.

    Conclusions:

    • The proposed algorithm provides a versatile and intuitive method for encoding and visualizing biological sequences.
    • This approach facilitates the visual and chemometric comparison of genetic data, aiding in evolutionary and functional studies.
    • The dimensionality flexibility of the algorithm makes it adaptable to various analytical needs in bioinformatics.