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Bioinformatics Advance Access published online on October 2, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl494
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 28, 2006
Revised August 23, 2006
Accepted September 22, 2006

Applications note

GenoProfiler: batch processing of high throughput capillary fingerprinting data

Frank M. You 1 *, Ming-Cheng Luo 1 *, Yong Qiang Gu 2, Gerard R. Lazo 2, Karin Deal 1, Jan Dvorak 1, and Olin D. Anderson 2 *

1 Department of Plant Sciences, University of California, Davis, CA 95616, USA
2 Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA

* To whom correspondence should be addressed.
Olin D. Anderson, E-mail: oandersn{at}pw.usda.gov


  Abstract

Summary: 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.

Availability: http://wheat.pw.usda.gov/PhysicalMapping/.

Associate Editor: Keith A Crandall

* The authors contribute equally to this work.


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