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United States Department of Agriculture

Agricultural Research Service

Title: Geno Profiler: Batch Processing of High Throughput Capillary Fingerprinting Data

Authors
item You, Frank - UC DAVIS
item Luo, Ming - UC DAVIS
item Gu, Yong
item Lazo, Gerard
item Deal, Karin - 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: January 15, 2007
Citation: You, F.M., Luo, M.C., Gu, Y.Q., Lazo, G.R., Thomas, C., McGuire, P.E., Dvorak, J., and Anderson, O.D. 2007. Genoprofiler: Automated processing of high throughput capillary fingerprinting data. Bioinformatics. 23:240-242.

Interpretive Summary: A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. This will assist laboratories involved in high-throughput fingerprinting techniques employing capillary electrophoresis. The ultimate results of this software provides properly formatted files suitable for processing by a software package named FPC which is used to assemble physical contigs from genome clones. The data provided to the software is dependent on the genome size of the organism of study. For a genome of 5000 Mb, up to 400,000 fingerprints would be used.

Technical Abstract: High-throughput fingerprinting techniques employing capillary electrophoresis place new demands on the editing of fingerprint files for the downstream contig assembly program, FPC. A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. The batch-processing module extracts the sized fragment information directly from the ABI raw trace files, or from data files exported from GeneMapper or other size calling software, removes the background noise and undesired fragments, and generates fragment size files compatible with the FPC software. With this technique, thousands of BAC clones can be fingerprinted per day. GenoProfiler is a Java-based cross-platform software package for fully automated processing of capillary fingerprint data generated by the ABI 3100/3700/3730 Genetic Analyzer. Dedicated algorithms were developed and implemented in a batch-processing module within the program. GenoProfiler also includes tools for data analysis, management, and quality control. These tools allow the viewing of chromatographs, remove fragment(s) originating from repeated sequences, eliminate substandard profiles, detect and eliminate cross-contamination of samples, and identify clones containing chloroplast DNA. The software has been successfully used in the wheat D-genome physical mapping project for the processing of approximately 300,000 large-insert BAC clones and is being used in more than 30 laboratories worldwide.

Last Modified: 4/20/2014
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