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United States Department of Agriculture

Agricultural Research Service

Title: Geno Profiler: Automated processing of high throughput capillary fingerprinting data

Authors
item You, Frank - UC DAVIS
item Ming-Cheng, Luo - UC DAVIS
item GU, YONG
item LAZO, GERARD
item Thomas, Carolyn - UC DAVIS
item Mcguire, Patrick - UC DAVIS
item Dvorak, Jan - UC DAVIS
item Anderson, Olin

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 22, 2006
Publication Date: October 2, 2006
Citation: You, F., Ming-Cheng, L., Gu, Y.Q., Lazo, G.R., Thomas, C., Mcguire, P.E., Dvorak, J., Anderson, O.D. 2006. Geno Profiler: Automated Processing of High Throughput Capillary Fingerprinting Data. Bioinformatics. 2:240-242.

Interpretive Summary: Bread wheat is one of the important staple crops in the world. However, because of its large genome size and polyploid nature, cloning of agronomic important genes for crop improvement remains as a challenge in wheat. Wheat bacterial artificial library represents a complete component of wheat genomic DNA that have been digested into small fragments and stored in E. coli for easy manipulation. A physical map for the wheat genome can be developed based on overlapping fingerprints of the BAC library clones. Such physical map will facilitate map-based cloning of genes important for agriculture. In this manuscript, a cross platform software application, GenoProfiler, was developed for automated editing of raw fingerprinting data generated by high throughput capillary sequencer such as ABI3100/3730. The software allows extraction and editing sized fragment information directly from ABI sequencer and generates fragment size files compatible with FPC software for downstream contig assembly. This software has been successfully examined in the wheat D genome physical map project funded by the National Science Foundation.

Technical Abstract: A cross-platform software application, GenoProfiler, was developed for automated editing of raw fingerprinting profiles generated by the ABI 3100/3700/3730 Genetic Analyzers. The batch-processing module extracts and edits sized fragment information directly from the ABI sample data files and generates fragment size files compatible with FPC software for downstream contig assembly. GenoProfiler also includes a set of tools for data visualization, analysis, management, and quality control. These tools allow users to view chromatograms, to analyze fragment size distribution, to eliminate vector fragment(s) and other undesirable fragment(s), to eliminate substandard profiles from a data set, and to detect and exclude potential cross-contaminations. The software creates a pipeline for high-throughput processing of capillary electrophoresis fingerprinting data. To evaluate the software, 165,573 clones from 3 BAC libraries of Aegilops tauschii (the source of the wheat D genome) were successfully processed. The generalized software is suitable for editing data in other physical mapping projects.

Last Modified: 9/10/2014
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