EcoGene

EcoGene provides curated genomic annotations and analysis tools for structural and functional characterization of Escherichia coli K-12 (MG1655(Seq)) and comparative bacterial genomics.

Key Features:

• Enhanced Genome Visualization: Advanced graphical representations of genome map features for Escherichia coli K-12 (MG1655(Seq)).
• Boolean Queries and Venn Diagrams: Supports complex Boolean queries and Venn diagram generation via EcoArray and EcoTopics or by inputting custom GeneSets.
• Primer Design Tool (PrimerPairs): Genome-wide design of clone and deletion primers.
• Customized Sequence Search (EcoBLAST): Tailored BLAST-based sequence searches optimized for Escherichia coli research.
• Cross-Referencing Capabilities: Cross Reference table linking synonymous gene and protein identifiers.
• Proteome Indexing with GO Terms: Proteome-wide indexing using Gene Ontology (GO) terms for functional annotation.
• Access to Extensive Genomic Data: EcoTools provides access to over 2000 complete bacterial genomes within the EcoGene-RefSeq database.
• Robust Database Infrastructure: Uses a MySql relational database for data storage.
• Literature Integration and Updates: Continuous literature surveillance with over 98,425 PubMed-Gene links and 5,415 PubMed-Topic links as of September 2012, with updates transmitted to Genbank (U00096) at NCBI.

Scientific Applications:

• Functional Genomics: Provides detailed gene function annotations and literature links to support interpretation of gene roles in Escherichia coli.
• Comparative Genomics: Access to EcoGene-RefSeq and over 2000 complete bacterial genomes supports comparative analyses of evolutionary relationships and conserved functions.
• Experimental Design: PrimerPairs and EcoBLAST support design and sequence-validation of cloning and deletion experiments.
• Data Integration and Analysis: Cross-referencing and GO term indexing enable integration of identifiers and functional data for pathway and systems analyses.

Methodology:

Annotations are updated via daily literature surveys, stored in a MySql relational database, and transmitted to Genbank (U00096) at NCBI.