Difference between revisions of "Croc CoGe"

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===Useful Links===
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=== About the Project  ===
  
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*[http://crocgenomes.org/ Croc Genomes Project] - The International Crocodilian Genomes Working Group (ICGWG) is leading a large-scale effort to use genomic methods to examine crocodilian biology.
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CoGe provides support for the International Crocodilian Genomes Working Group (ICGWG). ICGWG is leading a large-scale effort to use genomic methods to examine crocodilian biology. We have targeted the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus), and gharial (Gavialis gangeticus) for genome sequencing and have produced preliminary genome assemblies. Current genome assemblies are available on CoGe for easy comparative analyses.  
  
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* [http://crocgenome.hpc.msstate.edu/crocbase/index.php CrocBase] - Online resource for crocodilian genetics.
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== Available Resources  ==
  
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[https://genomevolution.org/CoGe/NotebookView.pl?nid=45 CoGe Croc Genomes Notebook] - CoGe Notebook containing 6 Croc genomes, for easy access to comparative genome analyses.
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{| cellspacing="1" cellpadding="1" border="1" align="left"
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|+ Table 1. Current croc genomes available on CoGe
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|-
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! scope="col" | Species<br>
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! scope="col" | Common Name<br>
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! scope="col" | Links<br>
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|-
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| Alligator mississippiensis<br>
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| American alligator<br>
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| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24821 Unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24853 Masked]<br>
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|-
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| Crocodylus porosus<br>
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| Saltwater crocodile<br>
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| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24820 Unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24851 Masked]<br>
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|-
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| Gavialis gangeticus
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| Indian gharial
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| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24819 Unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24855 Masked]<br>
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|}
  
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===Related Resources===
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<br clear=all>
  
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[[Bird CoGe]]
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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. <br>
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<br>
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The crocodile genomes are publicly available through CoGe and are collected into a notebook for easy access.<br>
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*[https://genomevolution.org/CoGe/NotebookView.pl?nid=45 Croc Genomes: Masked and Unmasked]
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<br>
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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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<br>
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More information on getting started, including tutoials on how to use CoGe tools, is here: https://genomevolution.org/wiki/index.php/New_to_CoGe
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== Useful Links  ==
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*[http://crocgenomes.org/ Croc Genomes Project] - Croc Genomes Project homepage
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*[http://crocgenome.hpc.msstate.edu/crocbase/index.php CrocBase] - Online resource for crocodilian genetics.
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*[https://genomevolution.org/CoGe/NotebookView.pl?nid=45 CoGe Croc Genomes Notebook] - CoGe Notebook containing Croc genomes, for easy access to comparative genome analyses.
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== Related Resources  ==
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*[[Bird CoGe]] - Bird genomes from the Avian Phylogenomics Initiative

Latest revision as of 13:04, 5 December 2014

About the Project

CoGe provides support for the International Crocodilian Genomes Working Group (ICGWG). ICGWG is leading a large-scale effort to use genomic methods to examine crocodilian biology. We have targeted the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus), and gharial (Gavialis gangeticus) for genome sequencing and have produced preliminary genome assemblies. Current genome assemblies are available on CoGe for easy comparative analyses.

Available Resources

Table 1. Current croc genomes available on CoGe
Species
 Common Name
 Links
Alligator mississippiensis
 American alligator
 Unmasked Masked
Crocodylus porosus
 Saltwater crocodile
 Unmasked Masked
Gavialis gangeticus Indian gharial Unmasked Masked


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.

The crocodile genomes are publicly available through CoGe and are collected into a notebook for easy access.


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, including tutoials on how to use CoGe tools, is here: https://genomevolution.org/wiki/index.php/New_to_CoGe

Useful Links

  • CrocBase - Online resource for crocodilian genetics.

Related Resources

  • Bird CoGe - Bird genomes from the Avian Phylogenomics Initiative
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