Difference between revisions of "Documentation"
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== Web Application Documentation == | == 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 | *[[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 | *[[FeatView]] Search for genomic features by name or description | ||
*[[SynMap]] Generate syntenic dotplots of any two genomes | *[[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 | *[[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=== | ===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 | *[[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 | *[[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 | + | <!-- *[[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. | ||
| − | *[[QuotaAlign]] Screen syntenic blocks | + | *[[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== | ==Linking to CoGe== | ||
| Line 30: | Line 40: | ||
*CoGe's [[Open-ended Analysis Network]] | *CoGe's [[Open-ended Analysis Network]] | ||
*[[CoGe Database]] | *[[CoGe Database]] | ||
| − | *[[ | + | *[[Web Services REST API ]] |
*[[GeLo]] Graphics Library | *[[GeLo]] Graphics Library | ||
| − | |||
*[[Gobe]] Flash Results Viewer (Used in Gevo) Documentation | *[[Gobe]] Flash Results Viewer (Used in Gevo) Documentation | ||
Latest revision as of 12:33, 15 September 2016
Contents
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
