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

Sequence alignment with tandem duplication

G Benson1

  • 1Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, New York 10029-6574, USA. benson@ecology.biomath.mssm.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 1, 1997
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

Thrombosis and Survival after Prothrombin Complex Concentrate Use to treat Oral Anticoagulant Associated Haemorrhage.

The Ulster medical journal·2026
Same author

PROTHROMBIN COMPLEX CONCENTRATE USE IN BELFAST HEALTH AND SOCIAL CARE TRUST.

The Ulster medical journal·2021
Same author

Profiles of exposure to potentially traumatic events in refugees living in Australia.

Epidemiology and psychiatric sciences·2021
Same author

Obesity in the global haemophilia population: prevalence, implications and expert opinions for weight management.

Obesity reviews : an official journal of the International Association for the Study of Obesity·2018
Same author

Age adjusted D-dimer in the Belfast Health and Social Care Trust: A retrospective study.

The Ulster medical journal·2018
Same author

Safety and effectiveness of room temperature stable recombinant factor VIIa in patients with haemophilia A or B and inhibitors: Results of a multinational, prospective, observational study.

Haemophilia : the official journal of the World Federation of Hemophilia·2017
Same journal

Mosquito Species and Gender Identification System Based on Artificial Intelligence and Image Processing Methods.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

This study introduces the DSI model for biological sequence comparison, incorporating tandem duplications alongside substitutions, insertions, and deletions. New algorithms are developed for aligning DNA sequences with tandem repeats, improving sequence analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional sequence alignment relies on the Substitution, Insertion, and Deletion (SI) model.
  • The SI model does not account for other significant mutational events like tandem duplications.
  • Tandem repeats are prevalent in genomes and implicated in diseases and gene regulation.

Purpose of the Study:

  • Introduce a new computational model, the Duplication, Substitution, Insertion, and Deletion (DSI) model.
  • Develop novel algorithms for biological sequence comparison and alignment that incorporate tandem duplications.
  • Enhance the analysis of DNA sequences containing tandem repeats.

Main Methods:

  • Developed the DSI model to include tandem duplication as a mutational event.

Related Experiment Videos

  • Designed exact and heuristic algorithms based on the DSI model.
  • Applied algorithms to DNA sequences containing tandem repeats.

    • Main Results:

    • The DSI model provides a more comprehensive framework for sequence evolution.
    • New algorithms demonstrate improved capability in aligning sequences with tandem repeats.
    • The developed methods offer enhanced tools for genomic analysis.

    Conclusions:

    • The DSI model represents a significant advancement over the SI model for sequence analysis.
    • The new algorithms facilitate more accurate comparison and alignment of DNA sequences with tandem repeats.
    • This work has implications for understanding genome evolution, disease mechanisms, and DNA regulation.