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Difference between revisions of "CMap"
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* [http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 Pristionchus pacificus Physical Map] | * [http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 Pristionchus pacificus Physical Map] | ||
* [http://medvet.angis.org.au/cmap/ Comparitive Location Database] | * [http://medvet.angis.org.au/cmap/ Comparitive Location Database] | ||
| − | * [http://soybeanbreederstoolbox.org | + | * [http://soybeanbreederstoolbox.org/index.php Soybean Breeders Toolbox] |
* [http://map.lab.nig.ac.jp:8080/cmap/ Composite Wheat Map] | * [http://map.lab.nig.ac.jp:8080/cmap/ Composite Wheat Map] | ||
* [http://peanutgenetics.tamu.edu/cmap/ PeanutMap] | * [http://peanutgenetics.tamu.edu/cmap/ PeanutMap] | ||
Revision as of 17:31, 13 May 2009
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.
Contents
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 (CVS)
- /cmap/README
- /cmap/Changes
- /cmap/INSTALL.pod
- /cmap/docs/ADMINISTRATION.pod
- /cmap/docs/CODE_OVERVIEW.pod
- /cmap/TODO
- /cmap/docs/attributes-and-xrefs.pod
- /cmap/docs/cmap-schema-desc.html
- CMAP Tutorial at Texas A & M
- CMap Version 2 Design
Also see the CMap FAQ.
Presentations
- 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
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
Patches
- See the SourceForge Patch List.
- 1.0: Patched schema creation file for Postgres: cmap.create.postgresql.
Mailing List
- gmod-cmap@lists.sourceforge.net: Discussion of development, installation problems, etc.
- gmod-cmap-commits@lists.sourceforge.net: Notification of CVS activity
- Subscribe to gmod-cmap
- gmod-cmap archives
