Difference between revisions of "Bird CoGe"

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(Created page with '==Bird CoGe and the Genome 10K and the Avian Phylogenomics Initiative== ===About the Project=== CoGe is providing support for the Avian Phylogenomics Initiative. This group has...')
 
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==Bird CoGe and the Genome 10K and the Avian Phylogenomics Initiative==
 
 
 
===About the Project===
 
===About the Project===
  
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===Available Resources===
 
===Available Resources===
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===Using the Resources on CoGe===
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The Comparative Genomics (CoGe) browser is designed to make it easy to find and compare genomic sequences, including multiple species and multiple versions of genomes. There is no single, linear workflow through the system. Instead, CoGe's tools allow you to access the system to find sequences of interest, and "hub" points to take you from one part of the system to another. This allows for ideas to be generated while working CoGe, and be able to quickly branch out to investigate any number of interesting phenomena you find.
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CoGe's web-tools have several applications for initiating an analysis:
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* [[OrganismView]]: Search and get an overview of an organism and its genomic information
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* [[CoGeBlast]]: Blast against any number of organisms using CoGe's Blast interface (supports Blast, and BlastZ).
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* [[FeatView]]: Search for genomic features by name or description
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* [[SynMap]]: Generate syntenic dotplots of any two genomes
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* [[GEvo]]: Compare multiple genomic regions using a variety of sequence comparison algorithms for high-resolution analysis to quickly identify patterns of genome evolution
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More information on getting started is here: https://genomevolution.org/wiki/index.php/New_to_CoGe
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Tutorials on how to use CoGe tools are here: https://genomevolution.org/wiki/index.php/New_to_CoGe

Revision as of 15:01, 4 December 2014

About the Project

CoGe is providing support for the Avian Phylogenomics Initiative. This group has sequenced genomes of over 50 avian species, including one species belonging to each major order. The goals of the project are to:

1) Perform phylogenomic analyses to decipher avian phylogeny;
2) Identify genetic changes as signatures of convergent selection, including in vocal learning species;
3) Sequence genomes of avian species that provide scientific value to the community, are national symbols, or endangered; and
4) Provide a public resource for scientist.

The project is partnered with other initiatives such as the Genome 10K (G10K) group to sequencing 10,000 vertebrate species in 10 years, a Copenhagen phylogenome group to decipher avian phylogeny, and the Beijing Genome Institute (BGI) to also decipher avian phylogeny and provide genomic resources. The project is coordinated by Erich Jarvis (Duke), Tom Gilbert (Copenhagen), and Goujie Zhang (BGI).

For more information about this project see: <add links to papers here after 12 Dec>

Available Resources

Using the Resources on CoGe

The Comparative Genomics (CoGe) browser is designed to make it easy to find and compare genomic sequences, including multiple species and multiple versions of genomes. There is no single, linear workflow through the system. Instead, CoGe's tools allow you to access the system to find sequences of interest, and "hub" points to take you from one part of the system to another. This allows for ideas to be generated while working CoGe, and be able to quickly branch out to investigate any number of interesting phenomena you find.


CoGe's web-tools have several applications for initiating an analysis:

  • 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

More information on getting started is here: https://genomevolution.org/wiki/index.php/New_to_CoGe

Tutorials on how to use CoGe tools are here: https://genomevolution.org/wiki/index.php/New_to_CoGe