Documentation

Web Application Documentation

CoGe Tools

• 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
• SynFind Identify syntenic regions against any set of genomes given a gene in one genome
• 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

• SynMap3D Visualize whole genome synteny across three genomes
• 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.
• QuotaAlign Screen syntenic blocks based on expected coverage
• CodeOn Tool for generating amino acid use charts binned by GC content of CDS sequences. Generated for a list of organisms or genomic features

Linking to CoGe

Since CoGe's tools are all web-based, it is easy to make URLs that link directly into CoGe's applications with specific genomic regions and data pre-loaded. This is useful for other web-based applications and pre-computed datasets.

• Linking to GEvo
• Linking to OrganismView
• Linking to GenomeView

Backend Documentation

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