Difference between revisions of "CMap"

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	CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data.		CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data.
	== Citation ==		== Citation ==
−	[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp458?ijkey=RH2dYR27nTL4Bw9&keytype=ref CMap 1.01: a comparative mapping application for the Internet.]	+	[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp458?ijkey=RH2dYR27nTL4Bw9&keytype=ref CMap 1.01: a comparative mapping application for the Internet.]
	Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.		Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.

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Revision as of 22:42, 19 August 2010

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Status

• Mature release
• Active development
• Active support

Resources

• CMap @ Gramene
• Tutorial @ Gramene
• Admin (perldoc)
• Other Doc
• Mailing List
• Download
• CMap3D
• 2008 SurveyTemplate:ComponentBoxEventsHeader
  
  

PAG XIX
15-19 Jan 2011

CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data.

Citation

CMap 1.01: a comparative mapping application for the Internet.

Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.

1. Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724,
2. Department of Plant Breeding and Genetics, Cornell University, Ithaca and
3. USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853, USA

Requirements

• Perl 5.6.0 or higher
• A web server with CGI capabilites (e.g., Apache 1.x or 2.x)
• A relational database, e.g. MySQL (4.0+), Sybase Adaptive Server Enterprise, PostgreSQL, SQLite or Oracle (9.x)
• libgd 2.0.28 and GD.pm 2.15
• Various Perl modules available on CPAN

Documentation

• Gramene CMap User Tutorial,

  Available in both PDF and PowerPoint formats.

• CMap_API (SVN)
• README
• Changes
• INSTALL.pod
• ADMINISTRATION.pod
• CODE_OVERVIEW.pod
• TODO
• attributes-and-xrefs.pod
• CMAP Schema
• CMAP Tutorial at Texas A & M
• CMap Version 2 Design

Also see the CMap FAQ.

Presentations

• Genome Visualization and Comparison using CMap and Circos, poster from Genome Informatics 2009
• The CMap Comparative Map Browser and Displaying Population distributions with GBrowse and PhyloGeoViz from the GMOD Workshop at SMBE 2009
• CMap and CMAE from November 2007 GMOD Meeting
• CMap Version 0.16 from June 2006 GMOD Meeting
• CMap Update 2005 from May 2005 GMOD Meeting
• Gramene Comparative Genome Views: How Can Gramene Leverage Rice For The Other Grasses? poster form 2005 Plant and Animal Genomics meeting.
• CMap Update 2003 from September 2003 GMOD Meeting.
• CMap: Visualization of Comparative Maps from May 2003 GMOD Meeting.

Downloads

From SourceForge.

Demo & Screenshots

See the Gramene Project for a production version.

Screenshots

Here are some sample maps from the Gramene Project.

Sites Using CMap

The following is a partial list of groups using CMap.

• Gramene: Comparative mapping resource for grasses (plant)
• NCGR's Legume Information System: A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons
• BeeBase: The Honey Bee genome database
• BASC: Brassica database
• GrainGenes
• MAGI
• Genome Database for Rosaceae
• Cotton Marker Database
• SCRI Plant Bioinformatics Group
• Pristionchus pacificus Physical Map
• Comparitive Location Database
• Soybean Breeders Toolbox
• Composite Wheat Map
• PeanutMap
• CottonDB
• TropGene

Code

• CMap SVN

Patches

• See the SourceForge Patch List.
• 1.0: Patched schema creation file for Postgres: {{SF_SVN|/cmap/trunk/sql/cmap.create.postgresql cmap.create.postgresql].

Mailing Lists

Contact

• Ken Youens-Clark
• Ben Faga

Logo

The CMap logo was created by Kathy Bracken, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.