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

SynBrowse: a synteny browser for comparative sequence analysis.

Xiaokang Pan1, Lincoln Stein, Volker Brendel

  • 1Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011-3260, USA.

Bioinformatics (Oxford, England)
|July 5, 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

Apollo 3: Multi-Species Genome Curation.

bioRxiv : the preprint server for biology·2026
Same author

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

Research square·2026
Same author

Proteins in the Genome Browser: Integration of Phylogenies, Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2.

Journal of molecular biology·2026
Same author

Application of Large Language Models for Annotating Genes into Reactome Pathways.

bioRxiv : the preprint server for biology·2026
Same author

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

bioRxiv : the preprint server for biology·2025
Same author

Setting up JBrowse 2 for Visualizing Genome Synteny.

Current protocols·2025
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

SynBrowse is a portable genome alignment visualization tool for comparative sequence analysis. It helps scientists identify homologous genes and structural features within and between species.

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Comparative sequence analysis is crucial for understanding evolutionary relationships.
  • A portable and generic tool is needed for visualizing and analyzing genome-wide sequence comparisons.

Purpose of the Study:

  • To develop SynBrowse, a synteny browser for visualizing and analyzing genome alignments.
  • To aid scientists in studying macrosynteny, microsynteny, and homologous genes.
  • To facilitate the identification of uncharacterized genes and novel genomic features.

Main Methods:

  • SynBrowse is a GBrowse (Generic Genome Browser) family software tool.
  • It utilizes open-source BioPerl modules and comprises a web-based front end and relational database back ends.

Related Experiment Videos

  • Databases store pre-computed alignments and genome annotations for comparative analysis.

    • Main Results:

    • SynBrowse enables visualization and analysis of genome alignments within and between species.
    • Users can search for syntenic blocks and examine relationships between genome annotations.
    • The tool supports identification of homologous genes, regulatory elements, and structural features.

    Conclusions:

    • SynBrowse offers a portable, configurable, and easily integrated solution for comparative genomics.
    • It enhances the study of genome structure and function through detailed visualization of sequence alignments.