LaneRuler 0.1 (Beta release) (Feb 22, 2007)
This is not a final release. Experimental releases should only be used for testing and development. Do not use these on production sites, and make sure you have proper backups before installing.
This is the first public release for LaneRuler. It is created from our repository at http://trac/lanetracker/browser/trunk revision 184.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Beta release |
|---|---|
| License | GPL |
A software package has been developed for the automated lane tracking in electrophoresis gels, with a focus on gels made for physical mapping of genomes. The lanes on such gels may not be straight and parallel due to physical handling of the gel, imperfect wells, temperature variations during the run, etc.. These deviations must be accounted for in order to accurately size the restriction fragments in each lane. The high throughput required by the projects at the BC Cancer Agency Genome Sciences Center (GSC) necessitate a full automation of this step. Thus, the package is also required to verify and correct its results automatically, and only prompting for user inspection for the extreme cases. With this package, the center of a lane is approximated with a piece-wise linear curve drawn between nodes identified for every subsection or zone of the lane, given that lane directions can only varies slowly across the gel. Automatic lane tracking is done in several steps, including: image processing to suppress noise and to fill in the space between bands along each lane; node locating to identify the centers of the lanes; node correction to detect and to make adjustment in areas that have poor data quality; results checking to draw attention to exceptional gels; and lane straightening to output a corrected image for band calling. The program, written in C and called LaneRuler, is in use in production mode at the GSC for the hydatidiform mole project and the lymphoma cancer project. In validation testing using Bacterial Artificial Chromosome (BAC) clones, the automatic lane tracking results gave band calling results that are comparable to those from manually supervised lane tracking results, achieving sensitivity and specificity of restriction fragment identification exceeding 95%. The package is undergoing continual development to response to the needs of the GSC. The current conception of the program is able to successfully process 96% of the gels with no human intervention.
