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GBrowse Population Displayand
CMap
SMBE 2009Ben Faga
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Population Data in GBrowse
Goal: Overlay population data from GBrowse on a Google Map
PhyloGeoViz is a mash up to display poplation data on a Google Map
PhyloGeoViz was a 2007 Google Summer of Code project by Yi-Hsin Erica Tsai at NESCent
Interface between GBrowse and PhyloGeoViz Available in GBrowse 2 development code
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Population Demo
http://localhost/cgi-bin/gb2/gbrowse/pop_demo/ Each population is a track with latitude and
longitude values
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GBrowse data in PhyloGeoViz
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Click Marker to Get Population Data
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PhyloGeoViz in a Pop-up Balloon
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PhyloGeoViz in a Pop-up Balloon
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Installation Requirements
GBrowse 2 (in development) PhyloGeoViz (Optional but highly recommended)
PHP Google Maps API Key
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GBrowse Data and Configuration
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Gbrowse/PhyloGeoViz Questions?
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What is CMap?CMap is a web-based, comparative map viewer
Data provided by the Gramene project (www.gramene.org)
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About CMap CMap is a web application that can be used to
display data to anyone with a web browser CMap is a component of the GMOD project
which was originally developed for Gramene CMap runs on a web server using Perl and is
compatible most database management systems
CMap is freely available, under the GPL or the Artistic License 2.0.
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Advantages of CMap(Why Use CMap?)
CMap is data type agnostic and can display comparisons of sequence data, physical data, genetic data, etc with each other.
CMap can be used to compare chromosomes of different species.
CMap can be used to display comparisons of different types of data to look for inconsistencies.
CMap is web based which makes sharing information as easy as sending a bookmark.
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Comparing Sequence Assembly Against Optical Map
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CMap Displaying Synteny
Data provided by the Gramene project (www.gramene.org)
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CMap Displaying a Sequence Assembly vs a FPC Maps
Data provided by the Gramene project (www.gramene.org)
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CMap Displaying a Sequence Assembly vs a FPC Maps
Data provided by the Gramene project (www.gramene.org)
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CMap Displaying a Sequence Assembly vs a FPC Maps
Data provided by the Gramene project (www.gramene.org)
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CMap Displaying a Sequence Assembly vs a FPC Maps
Data provided by the Gramene project (www.gramene.org)
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Dot Plot
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What CMap is Not:
GBrowse A sequence viewer (no sequence is imported) A tool for creating data (although it has a tool
for creating correspondences between features of the same name)
Easily googled for (use “GMOD CMap”)
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Importing Data
Tab DelimitedCMap GFF3
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Acknowledgments
Doreen Ware and the Ware Lab
Lincoln Stein and the Stein Lab
Gramene (www.gramene.org)
GMOD (www.gmod.org)
NESCent (www.nescent.org)
Google (www.google.com)
Yi-Hsin Erica Tsai (original author of PhyloGeoViz)
Ken Clark (original author of CMap)
www.gmod.org/CMap
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Live Demo(Time and Technology Permitting)
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GBrowse Alignment and Trace
Note: base differences are gray and insertions are represented by “)(“
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Menu System
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Asynchronous Comparative Maps Menu
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Heat Map Feature Glyph