GBrowse Population Display and CMap SMBE 2009 Ben Faga.

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Presentation transcript:

GBrowse Population Display and CMap SMBE 2009 Ben Faga

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

Population Demo Each population is a track with latitude and longitude values

GBrowse data in PhyloGeoViz

Click Marker to Get Population Data

PhyloGeoViz in a Pop-up Balloon

Installation Requirements GBrowse 2 (in development)‏ PhyloGeoViz (Optional but highly recommended)‏  PHP  Google Maps API Key

GBrowse Data and Configuration

Gbrowse/PhyloGeoViz Questions?

What is CMap? CMap is a web-based, comparative map viewer Data provided by the Gramene project (

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.

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.

Comparing Sequence Assembly Against Optical Map

CMap Displaying Synteny Data provided by the Gramene project (

CMap Displaying a Sequence Assembly vs a FPC Maps Data provided by the Gramene project (

CMap Displaying a Sequence Assembly vs a FPC Maps Data provided by the Gramene project (

CMap Displaying a Sequence Assembly vs a FPC Maps Data provided by the Gramene project (

CMap Displaying a Sequence Assembly vs a FPC Maps Data provided by the Gramene project (

Dot Plot

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”)‏

Importing Data Tab Delimited CMap GFF3

Acknowledgments Doreen Ware and the Ware Lab Lincoln Stein and the Stein Lab Gramene ( GMOD ( NESCent ( Google ( Yi-Hsin Erica Tsai (original author of PhyloGeoViz)‏ Ken Clark (original author of CMap)‏

Live Demo (Time and Technology Permitting)‏

GBrowse Alignment and Trace Note: base differences are gray and insertions are represented by “)(“

Menu System

Asynchronous Comparative Maps Menu

Heat Map Feature Glyph

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