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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

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

@@ Line 1: / Line 1: @@
 == Web Application Documentation ==
-===Main CoGe Entrance Pages===
+===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).
+*[[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]]
+<!-- *[[CoGeAlign]]  Generate multiple sequence alignments -->
+*[[FastaView]] Generate Fasta sequences of multiple genomic features
 *[[FeatList]] CoGe's tool for managing list of genomic features
-*[[FastaView]] Generate Fasta sequences of multiple genomic features
+*[[GenomeMap]]  Visually map genomic features to their genomic locations
+*[[EPIC-CoGe|GenomeView]] CoGe's interactive Genome Browser (also known as EPIC-CoGe)
+<!-- *[[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
 *[[SeqView]] Generate a Fasta sequence of a genomic region
-*[[GenomeView]] CoGe's interactive Genome Browser
+*[[SynMap3D]] Visualize whole genome synteny across three genomes
-*[[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.
 ==Linking to CoGe==
-Because 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.
+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]]
@@ Line 29: / Line 40: @@
 *CoGe's [[Open-ended Analysis Network]]
 *[[CoGe Database]]
-*[[CoGe Database API ]]
+*[[Web Services REST 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 [[Linking_to_GEvo | link]] against.
-*[[Linking to GEvo]]
-*[[Linking to OrganismView]]