Documentation

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Web Application Documentation

Top Menu Bar

  • Search Search CoGe's database to identify organisms, genomes, experiments, notebooks, and user groups
  • My Data Manage your genomes, experiments and notebooks. Upload new data and metadata. View analysis history.
  • My Account View account details. Upload new user icon.

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
  • LoadExperiment Load experimental quantitative, polymorphism, or alignment data for a genome in CoGe
  • LoadGenome Add your own genome for use with CoGe's various tools

Additional CoGe Pages

  • CodeOn Tool for generating amino acid use charts binned by GC content of CDS sequences. Generated for a list of organisms or genomic features
  • FastaView Generate Fasta sequences of multiple genomic features
  • FeatList CoGe's tool for managing list of genomic features
  • GenomeMap Visually map genomic features to their genomic locations
  • GenomeView CoGe's interactive Genome Browser (also known as EPIC-CoGe)
  • MatrixView View alignment scoring matrices.
  • QuotaAlign Screen syntenic blocks based on expected coverage
  • SeqView Generate a Fasta sequence of a genomic region
  • SynMap3D Visualize whole genome synteny across three genomes
  • tRNAView Search for tRNAs in genomes and genomic sequence

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.

Backend Documentation