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Related Experiment Video

Updated: May 10, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes.

Jindan Zhou¹, Andrew J Richardson, Kenneth E Rudd

¹Department of Biochemistry and Molecular Biology, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA. j.zhou1@miami.edu

Bioinformatics (Oxford, England)

|June 6, 2013

Summary

This summary is machine-generated.

EcoGene.org provides daily updates for the Escherichia coli K-12 MG1655 genome, enhancing annotation accuracy. A new resource, EcoGene-RefSeq, extends these tools to over 2400 prokaryotic genomes in the RefSeq database.

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Last Updated: May 10, 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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Published on: August 20, 2021

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

EcoGene.org is a dedicated genome database for Escherichia coli K-12 substrain MG1655.
It is updated daily with information from biomedical literature and in-house analysis.
EcoGene contributes significantly to annotation updates for the MG1655 Genbank record.

Purpose of the Study:

To develop EcoGene-RefSeq as a standalone internet resource.
To facilitate the use of EcoGene-based tools on prokaryotic genome records.
To leverage the extensive RefSeq database for broader genomic analysis.

Main Methods:

Daily revision of EcoGene.org using literature and in-house analysis.
Integration of EcoGene data with the National Center for Biotechnology Information's Reference Sequence (RefSeq) database.
Development of a web interface for EcoGene-RefSeq.

Main Results:

EcoGene serves as a primary source for MG1655 Genbank record annotation updates.
The RefSeq database contains over 2400 completed prokaryotic genome records.
EcoGene-RefSeq is being developed to apply EcoGene tools across these RefSeq records.

Conclusions:

EcoGene-RefSeq will enhance the utility of EcoGene tools for a wide range of prokaryotic genomes.
This resource supports community-driven annotation efforts.
It provides a valuable platform for comparative genomics and functional analysis.