CMap

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Description
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.
Demo
See the Gramene Project for a production version.
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
Downloads
From SourceForge.
Screenshots
Here are some sample maps from the Gramene Project. Click to view a larger version.

[[files/cmap_sample1.jpg Cmap sample1t.jpg]]

[[files/cmap_sample2.jpg Cmap sample2t.jpg]]

[[files/cmap_sample3.jpg Cmap sample3t.jpg]]

Sites 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
Code
Patches
Mailing List
Contact
[Ken Youens-Clark].
[Ben Faga].


Attachment Size

cmap_sample1.jpg

70.82 KB

cmap_sample1t.jpg

7.48 KB

cmap_sample2.jpg

91.47 KB

cmap_sample2t.jpg

11.21 KB

cmap_sample3.jpg

65.43 KB

cmap_sample3t.jpg

7.44 KB
Retrieved from "http://gmod.org/mediawiki/index.php?title=CMap&oldid=107"
Facts about "CMap"RDF feed
Available on platformweb +
Date published2009 +
Has DOI10.1093/bioinformatics/btp458 +
Has PMCIDPMC2773250 +
Has PMID19648141 +
Has URLhttp://sourceforge.net/projects/gmod/files/cmap/ +, https://gmod.svn.sourceforge.net/svnroot/gmod/cmap +, http://www.gramene.org/db/cmap +, http://www.gramene.org/cmap +, http://www.comparative-legumes.org/ +, http://racerx00.tamu.edu/cgi-bin/cmap/viewer +, http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi +, http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 +, http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info +, http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 +, http://www.cottonmarker.org/ +, http://bioinf.scri.sari.ac.uk/ +, http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM%3Bref_map_aids=109 +, http://medvet.angis.org.au/cmap/ +, http://soybeanbreederstoolbox.org/index.php +, http://map.lab.nig.ac.jp:8080/cmap/ +, http://peanutgenetics.tamu.edu/cmap/ +, http://www.cottondb.org/cmap/ +, http://tropgenedb.cirad.fr + and http://cricket.ornl.gov/cgi-bin/cmap/map_set_info +
Has authorYouens-Clark K +, Faga B +, Yap IV +, Stein L + and Ware D +
Has descriptionComparative mapping resource for grasses (plant) +, A publicly accessible legume resource that will integrate genetic and molecular data from multiple legume species and enable cross-species comparisons +, The Honey Bee genome database +, Brassica database + and A browser-based tool for the visual comparison of various maps (sequence, genetic, etc.) from any number of species. The CMap package also includes tools for curating map data. +
Has development statusinactive +
Has input formattab-delimited + and GFF +
Has licenceGPL +
Has logoCMapLogo-horiz.png +
Has output formattab-delimited +
Has publication detailsBioinformatics (Oxford, England) 25: 3040-2 +
Has software maturity statusmature +
Has support statusactive +
Has titleGramene +, NCGR's Legume Information System +, BeeBase +, BASC +, 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 +, Populus at Oak Ridge + and CMap 1.01: a comparative mapping application for the Internet. +
Has topicCMap +
Is open sourceYes +
Link typedownload +, source code +, demo server +, public server + and wild URL +
Published inBioinformatics (Oxford, England) +
Release date2002 +
Tool functionality or classificationGenome Visualization & Editing +, Comparative Genome Visualization + and Database schema +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.CMap#http://sourceforge.net/projects/gmod/files/cmap/ +, CMap#https://gmod.svn.sourceforge.net/svnroot/gmod/cmap +, CMap#http://www.gramene.org/db/cmap +, CMap#http://www.gramene.org/cmap +, CMap#http://www.comparative-legumes.org/ +, CMap#http://racerx00.tamu.edu/cgi-bin/cmap/viewer +, CMap#http://bioinformatics.pbcbasc.latrobe.edu.au/basc/cgi-bin/index.cgi +, CMap#http://rye.pw.usda.gov/cgi-bin/cmap/map_set_info?map_set_aid=Barley_consensus_2003 +, CMap#http://magi.plantgenomics.iastate.edu/cgi-bin/cmap/map_set_info +, CMap#http://www.bioinfo.wsu.edu/cgi-bin/gdr/cmap/map_set_info?map_set_aid=17 +, CMap#http://www.cottonmarker.org/ +, CMap#http://bioinf.scri.sari.ac.uk/ +, CMap#http://www.pristionchus.org/cgi-bin/cmap/viewer?ref_map_set_aid=PM;ref_map_aids=109 +, CMap#http://medvet.angis.org.au/cmap/ +, CMap#http://soybeanbreederstoolbox.org/index.php +, CMap#http://map.lab.nig.ac.jp:8080/cmap/ +, CMap#http://peanutgenetics.tamu.edu/cmap/ +, CMap#http://www.cottondb.org/cmap/ +, CMap#http://tropgenedb.cirad.fr + and CMap#http://cricket.ornl.gov/cgi-bin/cmap/map_set_info +