Difference between revisions of "Documentation"
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*[[HSPView]] Viewing regions of sequence similarity as identified through a variety of tools in CoGe using a variety of sequence comparison algorithms | *[[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. | *[[MatrixView]] View alignment scoring matrices. | ||
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| + | ==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. | ||
| + | *[[Linking to GEvo]] | ||
| + | *[[Linking to OrganismView]] | ||
| + | *[[Linking to GenomeView]] | ||
== Backend Documentation == | == Backend Documentation == | ||
Revision as of 19:50, 21 January 2010
Contents
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.
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.
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.
