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Related Concept Videos

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Updated: Feb 18, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Synima: a Synteny imaging tool for annotated genome assemblies.

Rhys A Farrer1,2

  • 1Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK. rfarrer@broadinstitute.org.

BMC Bioinformatics
|November 23, 2017
PubMed
Summary

Synteny Imaging tool (Synima) visualizes genome-wide synteny for evolutionary studies. This open-source Perl tool generates publication-quality figures from ortholog data, aiding comparative genomics research.

Keywords:
Imaging toolOrthologySyntenyVisualization

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Area of Science:

  • Comparative genomics
  • Evolutionary biology
  • Bioinformatics

Background:

  • Ortholog prediction and synteny visualization are crucial for understanding genome evolution.
  • Existing tools for multi-genome synteny visualization are limited.

Purpose of the Study:

  • To present Synima, a novel standalone tool for visualizing genome-wide synteny.
  • To provide a user-friendly pipeline for synteny analysis.

Main Methods:

  • Synima utilizes Perl and R for visualization.
  • Input data includes orthologs from reciprocal best BLAST hits or OrthoMCL, and DAGchainer.
  • Configurable parameters allow customization of output figures.

Main Results:

  • Synima generates genome-wide synteny overviews in PDF format.
  • The tool is efficient, running quickly from the command line.
  • Customizable graphical parameters ensure publication-quality figures.

Conclusions:

  • Synima is a valuable open-source tool for visualizing synteny between multiple annotated genomes.
  • It facilitates the study of evolutionary processes like genome expansion and rearrangements.