Documentation

Web Application Documentation

Main CoGe Entrance Pages

• OrganismView Search and get an overview of an organism and its genomic information
• CoGeBlast Blast against any number of organisms using CoGe's Blast interface (supports Blast, and BlastZ).
• FeatView Search for genomic features by name or description
• SynMap Generate syntenic dotplots of any two genomes
• GEvo Compare multiple genomic regions using a variety of sequence comparison algorithms for high-resolution analysis to quickly identify patterns of genome evolution

Additional CoGe Pages

• FeatList CoGe's tool for managing list of genomic features
• FastaView Generate Fasta sequences of multiple genomic features
• SeqView Generate a Fasta sequence of a genomic region
• GenomeView CoGe's interactive Genome Browser
• CoGeAlign Generate multiple sequence alignments
• GenomeMap Visually map genomic features to their genomic locations
• tRNAView Search for tRNAs in genomes and genomic sequence
• HSPView Viewing regions of sequence similarity as identified through a variety of tools in CoGe using a variety of sequence comparison algorithms
• MatrixView View alignment scoring matrices.

Backend Documentation

• CoGe's Open-ended Analysis Network
• CoGe Database
• CoGe Database API
• GeLo Graphics Library
• Genome Browser Documentation
• Gobe Flash Results Viewer (Used in Gevo) Documentation

Linking to CoGe

Since CoGe is a web-based application, its tools can be connected to one another using web links (URLs). As such, it is relatively straight-forward for links from other applications and data-sets to be created. For example, GEvo is a popular tool to link against.

• Linking to GEvo