A software package, named LaneRuler, has been developed for the automated lane tracking in electrophoresis gels, with a focus on gels for DNA fingerprinting. The lanes on such gels may not be straight and parallel due to various reasons, and these deviations must be accounted for in order to accurately size the restriction fragments in each lane. In order to meet the high throughput requirements by the projects at the British Columbia Cancer Agency Genome Sciences Center (GSC), the software has capability to verify and correct its results automatically, and prompting for user inspection only for extremely abnormal cases. In validation testing using Bacterial Artificial Chromosome (BAC) clones, the automatic lane tracking results gave restriction fragment sizing results that are comparable to those from manually supervised lane tracking results, achieving sensitivity and specificity of restriction fragment identification exceeding 95%. The current conception of the program is able to successfully process 96% of the gels with no human intervention.
The software has also given good results with electrophoresis gel for polymerase chain reaction (PCR) products and for cDNA.
LaneRuler 1.1 (Beta release) (Apr 23, 2007)
LaneRuler with adjustment interface, gzipped tarball
As a result of testing with cDNA and PCR gels, the algorithm has been expanded to give better support for those types of gels while not affecting the ability to process production type gels. Most notably, the generic spacing search has been modify to first only look for lane spacing, and not marker spacing. This improved results when there are few markers and when not all the lanes are loaded. Overall the code has also been better commented. Doxygen documentation is included.
LaneRuler 0.1 (Beta release) (Feb 22, 2007)
This is the first public release for LaneRuler.