Abstract
Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT) applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: (1) a family tree view which displays a color-coded family tree for an individual, (2) a sequential list of crosses, and (3) a list of crosses matching user-defined search criteria. Each feature contains options to specify the number of records shown and the latter two contain an option to filter results by the owner of the cross. The family tree feature is interactive, displaying a popup box with genetic information when the user mouses over an individual and allowing the user to draw a new tree by clicking on any individual in the current tree. The applet is written in JavaScript and reads genetic records from a tab-delimited text file on the server, so it is cross-platform, can be accessed by anyone with an Internet connection, and supports almost instantaneous generation of new trees and table lists. Researchers can use the tool with their own genetic cross records for any sexually reproducing organism. No additional software is required and with only minor modifications to the script, researchers can add their own custom columns. GRFT’s speed, versatility, and low overhead make it an effective and innovative visualization method for genetic records. A sample tool is available at http://stanford.edu/walbot/grft-sample.html.
Highlights
Researchers whose model organism reproduces sexually must keep track of each cross performed in order to trace lineages, determine the genetic make-up of specific individuals, and track the progeny of an individual
To address the need for an accessible and interactive family tree tool, we have developed a JavaScript applet named genetic records family tree (GRFT), that requires no additional software or database installations
MATERIALS AND METHODS The genetic records data displayed by the tool are read from a tabdelimited text file created by the researcher and saved on a web server
Summary
Researchers whose model organism reproduces sexually must keep track of each cross performed in order to trace lineages, determine the genetic make-up of specific individuals, and track the progeny of an individual. The most common choices are Microsoft Excel and general purpose database applications such as MS Access or FileMaker Pro because of wide availability, familiarity of use, and, in the case of Excel, an overlap with the data gathering, and analysis features. These general use tools allow searches to find crosses of interest, determining the lineage of an individual requires multiple lookups, patience, and often a sheet of paper to outline a clear graphical pedigree or “family tree.”. Some software packages to display family trees already exist, including Pedigraph, PediTree, and CraneFoot. These tools generate static pictures of family trees rather than providing an interactive interface for exploring them and generally require local installation (Van Berloo and Hutten, 2005; Mäkinen, 2006; Garbe and Da, 2008)
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