Documentation

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Revision as of 16:07, 12 February 2016 by Asherkhb (Talk | contribs) (Additional CoGe Pages)

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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

  • 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.

Backend Documentation