Author:
Cooper M L,Maffitt D R,Parsons J D,Hillier L,States D J
Abstract
Software to track sample lanes automatically in four-color, fluorescence-based, electrophoretic gel images has been developed for application in large-scale DNA sequencing projects. Lanes and lane boundaries are tracked by analyzing a first difference approximation to the gradient of a vertically integrated and processed "brightness" profile. Initially lanes are located in a region of the gel image selected for good horizontal lane spacing and signal strength. The software uses models of expected lane and interlane spacing and lateral lane behavior to maintain accurate tracking on imperfect gels. In areas where intensity-based tracking is difficult, interpixel column correlation is also used to locate and define lane features. Summary statistics and compressed-in-time images are generated for user evaluation of tracking performance. The software developed has been tested successfully on gel images with degradations including significant horizontal lane motion (curving) and image artifacts, and is now in full-scale use in our sequencing projects.
Publisher
Cold Spring Harbor Laboratory
Subject
Genetics(clinical),Genetics
Reference11 articles.
1. Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis
2. A graph theoretic approach to the analysis of DNA sequencing data.;Genome Res.,1987
3. Blanchard, A. 1993. “Sequence-specific effects on the incorporation of dideoxynucleotides by a modified T7 polymerase.” Ph.D. thesis, California Institute of Technology, Pasadena, CA.
4. Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores.
5. An adaptive, object oriented strategy for base calling in DNA sequence analysis
Cited by
10 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献
1. Automatic Lane Segmentation in TLC Images Using the Continuous Wavelet Transform;Computational and Mathematical Methods in Medicine;2013
2. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images;IEEE Transactions on Automation Science and Engineering;2010-07
3. The technology tour de force of the Human Genome Project;Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics;2005-04-15
4. Microsatellite Genotyping;Molecular Genetic Epidemiology — A Laboratory Perspective;2002
5. Cross-talk filtering in four dye fluorescence-based DNA sequencing;Electrophoresis;2000-08-01