GeConT 2

GeConT 2 visualizes genomic context and orthologous relationships in fully sequenced bacterial genomes to support comparative and functional analysis.

Key Features:

• Genomic context visualization: Visualizes individual genes and groups of genes together with their genomic neighborhoods in fully sequenced bacterial genomes.
• Orthology mapping: Displays orthologous relationships across bacterial species to highlight conserved gene sets.
• Database integration: Integrates annotations from COG (Clusters of Orthologous Groups), Pfam and KEGG.
• Sequence retrieval: Retrieves nucleotide and protein sequences for specified genes and their adjacent regulatory regions (5' and 3').
• Multi-level graphical representation: Produces graphical outputs that combine gene function, phylogenetic distribution and genomic context.

Scientific Applications:

• Microbial genomics: Analyze gene organization and content within bacterial genomes.
• Comparative genomics: Compare genomic neighborhoods and orthologous gene sets across bacterial species.
• Evolutionary biology: Investigate conservation and evolution of gene order and functional modules.
• Functional annotation: Support annotation of gene function using integrated COG, Pfam and KEGG evidence.
• Regulatory sequence analysis: Study 5' and 3' adjacent regions to inform analyses of gene regulation and expression patterns.

Methodology:

Integrates annotations from COG, Pfam and KEGG, retrieves gene and adjacent 5' and 3' sequences, and generates graphical representations of genes, gene groups and their orthologous relationships across bacterial genomes.