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

GECO--linear visualization for comparative genomics.

C T Kuenne1, R Ghai, T Chakraborty

  • 1Institute of Medical Microbiology, Justus-Liebig-University Frankfurter Strasse 107, D-35392 Giessen, Germany.

Bioinformatics (Oxford, England)
|November 2, 2006
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

Endothelial ENaC as a repressor of oxidative stress and a guardian of lung capillary barrier function in bacterial and viral pneumonia.

Frontiers in physiology·2025
Same author

Occurrence and trends of Clostridioides difficile infections in hospitalized patients: a prospective multi-centre cohort study in six German university hospitals, 2016-2020.

The Journal of hospital infection·2024
Same author

Generation and functional characterization of recombinant Porphyromonas gingivalis W83 FimA.

Journal of biotechnology·2021
Same author

Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042.

Scientific reports·2020
Same author

Light controlled cell-to-cell adhesion and chemical communication in minimal synthetic cells.

Chemical communications (Cambridge, England)·2019
Same author

Age and experience dependent changes in Egr-1 expression during the ontogeny of the context preexposure facilitation effect (CPFE).

Neurobiology of learning and memory·2018

GECO software visualizes multiple prokaryotic genomes linearly, aiding in the detection of genomic irregularities. This tool helps researchers identify horizontally transferred genes and other anomalies in microbial genomes.

Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • Understanding phylogenetic and functional relationships between prokaryotic species requires correlating and displaying qualitative and quantitative data.
  • Existing methods may lack efficient visualization tools for comparative genomics.

Purpose of the Study:

  • To present GECO, a novel client/server software for linear visualization of multiple prokaryotic genomes.
  • To enable the identification of genomic irregularities and evolutionary events in microbial genomes.

Main Methods:

  • GECO utilizes a client/server architecture to dynamically generate .png or .pdf images for genome visualization.
  • Ortholog relations are calculated using BLASTCLUST and displayed via color coding.
  • Genomic irregularities are identified by analyzing anomalous Guanine-Cytosine (G/C) composition.

Related Experiment Videos

Main Results:

  • GECO provides a linear visualization of multiple genomes, facilitating comparative analysis.
  • The software effectively displays ortholog relationships through color-coded representations.
  • Anomalous G/C composition can be readily identified, highlighting potential genomic variations.

Conclusions:

  • GECO is a valuable tool for researchers studying microbial genomics.
  • The software aids in the detection of horizontally transferred genes, pseudogenes, and insertions/deletions.
  • GECO enhances the interpretation of phylogenetic and functional relationships in related microbial genomes.