Welcome to EcoGene 3.0

EcoGene 3.0 is a new web interface for EcoGene.org built using the Drupal open source website software. EcoGene 2.0 and EcoGene 3.0 both present data from our daily-updated MySql relational database. Some of the scope and content of EcoGene.org will be available only through EcoGene 3.0. EcoGene 2.0 will remain available via a link on the EcoGene 3.0 home page for those who might prefer to continue using it. Please report any problems you find with EcoGene 3.0 to krudd@med.miami.edu.

Please cite the following reference for this resource: Jindan Zhou and Kenneth E. Rudd (2013) EcoGene 3.0 Nucleic Acids Research, 41 (D1): D613-D624.

EcoGene 2.0

New Features
By The Numbers
  • Gene Interval Updater is a tool that can be used to convert U00096.2 gene (and feature) genomic addresses to U00096.3 coordinates. The MG1655(Seq) [ATCC 700926] represented in Genbank U00096.2 [4,639,675 bp] has several sequence errors, including two missed IS element insertions, that were reported in 2012 by Freddolino et al. [pmid: 22081388]. We have confirmed these DNA sequence errors and corrected them, creating U00096.3 [4,641,652 bp]. MG1655(Seq) has three previously unknown gene mutations, in crl, gatC and glpR; two sequencing errors in ylbE were corrected, including a frameshift error that restored this ORF previously thought to be a pseudogene.

  • GeneSets Venn diagram and Boolean Query is a tool for performing Boolean query comparisons using GeneSets, which are collections of genes clustered by EcoTopics, EcoArray or user-uploaded gene lists. Venn diagram is an interactive graphic presentation of Boolean query comparisons using or two or three GeneSets.

  • Circle Maps is an interactive drawing tool for displaying genes on a circular chromosome map. Genes can be added directly on the Circle Maps page. Alternatively, Circle Maps can be accessed directly from EcoSearch results, TopicPages or EcoArray experimental data pages. A maximum of 250 genes can be displayed on the circle maps.

  • EcoGene-RefSeq is developed to facilitate the usage of EcoGene‚Äôs graphic presentations and tools with other genomes. Currently, 2089 complete bacterial genomes from the NCBI RefSeq project are accessible via EcoGene-RefSeq.

  • Cross Reference Mapping and Download is created for user access to many accession numbers, gene names and synonyms.

  • More details are available on the EcoTools page.

  • No front page content has been created yet.