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Bioinformatics Advance Access originally published online on October 2, 2006
Bioinformatics 2007 23(2):240-242; 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

GenoProfiler: batch processing of high-throughput capillary fingerprinting data

Frank M. You 1,{dagger}, Ming-Cheng Luo 1,{dagger}, 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.


  Abstract

Summary: High-throughput content 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/

Contact: oandersn{at}pw.usda.gov

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Keith A Crandall

Received on April 28, 2006; revised on August 23, 2006; accepted on September 22, 2006

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